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Whole Genome Sequencing identifies homozygous BRCA2 deletion guiding
treatment in de-differentiated prostate cancer
Karin Purshouse1~, Anna Schuh2~, Benjamin P Fairfax1, 5, Sam Knight3, Pavlos
Antoniou2, Helene Dreau2, Niko Popitsch3, Kevin Gatter4, Ian Roberts5, Lisa
Browning6, Zoe Traill7, David Kerr1, Clare Verrill6, Mark Tuthill1, Jenny C
Taylor2,3*, Andrew Protheroe1*
~ joint first authors
* Joint senior authors
1 - Oxford Cancer and Haematology Centre, Churchill Hospital, Headington, Oxford, OX3 7LE, UK.
2- Oxford National Institute for Health Research, Biomedical Research Centre/NHS Translational
Diagnostics Centre, The Joint Research Office, Block 60, The Churchill Hospital, Old Road,
Headington, Oxford, OX3 7LE, UK
3- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3
7BN, UK
4- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University
of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
5- Molecular Oncology and Haematology Unit, Weatherall Institute of Molecular Medicine, John
Radcliffe Hospital, Oxford, OX3 9DS, UK
6- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS
Foundation Trust, Oxford, OX3 9DU, UK.
7- Department of Radiology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation
Trust, Oxford, OX3 9DU, UK. Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Abstract
Whole genome sequencing (WGS) has transformed the understanding of the
genetic drivers of cancer and is increasingly being used in cancer medicine to
identify personalised therapies. Here we describe a case where the application of
WGS identified a tumoural BRCA2 deletion in a patient with aggressive
dedifferentiated prostate cancer that was repeat biopsied after disease
progression. This would not have been detected by standard BRCA testing and it
lead to additional treatment with a maintenance PARP inhibitor following
platinum based chemotherapy. This case demonstrates that repeat biopsy upon
disease progression and application of WGS to tumour samples has meaningful
clinical utility and the potential to transform outcomes in patients with cancer.
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Introduction
The role of whole genome sequencing (WGS) in identifying targetable mutations
in cancer remains one of the greatest hopes in achieving personalised cancer
therapy. Its role in patients with advanced treatment-resistant cancer by
rebiopsying patients at the point of progression has not been fully explored.
Most prostate cancers are adenocarcinomas which are sensitive to androgen
deprivation therapy. It is thought that androgen receptor-deplete
neuroendocrine cells, which are few in number and normally lie quiescent, can
flourish due to a cascade of molecular events, resulting in neuroendocrine
dedifferentiation and androgen therapy-resistant prostate cancer (Li et al., 2013;
Li et al., 2016). Dedifferentiation from adenocarcinoma to small cell carcinoma is
also recognised in EGFR-mutant lung cancer (Sequist LV et al., 2011).
Mutations in DNA repair genes are an important feature of many cancers and are
associated with an advanced, aggressive phenotype in prostate cancer (Robinson
et al, 2015; Cancer Genome Atlas Research Network, 2015; Mateo et al, 2015).
Germline BRCA mutations and their clinical association with breast and ovarian
cancer are well known, although there is an associated increased risk of other
malignancies such as stomach and pancreatic cancer (Friedenson., 2005). The
increased prevalence of prostate cancer in patients with germline BRCA1 and 2
mutations has prompted consideration of prostate cancer screening in such
patients by the IMPACT screening study (Bancroft et al., 2014).
Identification of somatic BRCA mutations in breast and ovarian cancer has been
driven by the option of Poly-ADP-Ribose (PARP) inhibitor therapy for patients
with BRCA mutations (Hennessy et al., 2009; Winter et al., 2016). Most BRCA Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
mutations identified in patients with prostate cancer are somatic, and, compared
with low mutation levels in early prostate cancer, around 15% of patients with
metastatic androgen therapy-resistant prostate cancer harbour functionally
relevant somatic mutations or deletions in BRCA1 or 2 (Robinson et al., 2015).
Current recommendations regarding role for rebiopsy in prostate cancer focus
on patients for whom an active surveillance approach is being pursued, although
the most recent European Association of Urology (EAU) - European Society for
Radiotherapy & Oncology (ESTRO) - International Society of Geriatric Oncology
(SIOG) (EAU-ESTRO-SIOG) Guidelines note the importance of biopsy at the point
of biochemical relapse in prostate cancer, ideally 18-24 months after treatment
(Cornford et al., 2016). Early rebiopsy or genome sequencing either at initial
biopsy or rebiopsy on disease progression do not have a standard role in
management. Here we present a case report of a patient with prostate cancer in
whom rebiopsy and WGS at the point of disease progression had a significant
and ongoing clinical impact due to the identification of a tumoural BRCA2
deletion not present in the initial biopsy.
Results
Clinical presentation and family history
A 63-year-old previously well man presented with a history of weight loss and
hip pain. The family history was relevant for breast cancer only with the
patient’s mother, maternal aunts and sister having developed breast cancer.
Blood tests demonstrated an elevated prostate specific antigen (PSA) 2900 μg/L
(<4.0 μg/L), alkaline phosphatase (ALP) 2361 IU/L (44 to 147 IU/L) and a
reduced Hb 10.8 g/dL (13.5 to 17.5g/dL). A CT scan of his body and whole body Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
MRI imaging demonstrated a primary prostate cancer with bone and pulmonary
metastases (Fig 1a). A prostate biopsy confirmed adenocarcinoma with a
Gleason score of 8 (4+4) (Fig 2a,b). He was referred to oncology and started
androgen-deprivation therapy (ADT) with bicalutamide and goserelin (Zoladex)
injections.
The patient had an initial PSA response to testosterone deprivation and within
three months the patient had gained weight with an unchanged performance
status (PS) of one. His PSA and ALP fell to 189.6 μg/L and ALP to 1516IU (Fig 3).
However over the following weeks he clinically deteriorated with increasing pain
in his right hip and upper leg. MRI imaging of his spine indicated progression of
the bony metastases causing L4 nerve root compression (Fig 1b). He was treated
with five fractions of radiotherapy to his thoracic (20Gy, 5 fractions) and lumbar
(18Gy, 5 fractions) spine and, given the radiographic progression, he commenced
palliative docetaxel chemotherapy.
In the subsequent weeks, the patient’s clinical condition deteriorated despite the
docetaxel treatment. His performance status quickly declined from 1 to 3. He
experienced increasing pain from bony metastases and developed urinary
retention requiring the insertion of a urinary catheter. Despite a fall in his ALP
and PSA (Fig 3) an MRI performed at this time indicated further progressive
bony metastatic disease (Fig 1c).
Given the rapid clinical progression was atypical for adenocarcinoma, a further
biopsy was taken from an expanding rib metastasis. This demonstrated
metastatic small cell carcinoma positive for panCK and TTF1, but negative for Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
other traditional markers of small cell carcinoma such as 34BE12, CD56,
synaptophysin and chromogranin (Fig 2c,d).
Genomic Analysis
An established research programme at the Oxford Molecular Diagnostics Centre,
a CPA (Clinical Pathology Accreditation - http://www.oxford-translational-
molecular-diagnostics.org.uk) institute, aims to integrate genomic analysis into
routine clinic care. WGS was discussed with the patient who consented to have
both germline and tumour DNA sequencing performed from a fresh tumour
biopsy.
Within the tumour, WGS identified two large genomic regions of copy neutral
loss of heterozygosity, 41 genomic regions with acquired copy number gains
(10/41 with more than one additional copy) and 56 with acquired copy number
losses, including four separate regions displaying homozygous loss in copy
number. One such homozygous loss was observed spanning ~1.68 Mb of
chromosome 13 from 13q12.3-q13.1. This large homozygous deletion includes
21 separate genes or non-coding RNAs including BRCA2 (Fig 4). Despite the
family history of breast cancer, no known pathogenic BRCA1 or BRCA2 germline
variants were identified. A summary of the mutation analysis is shown in table
1, and a more detailed variant table for the gene of interest, BRCA2, in table 2.
Treatment Outcome
Given the transition in histopathology from adenocarcinoma to small cell
carcinoma of the prostate the patient commenced a trial of etoposide and
carboplatin chemotherapy. This resulted in a rapid improvement both clinically, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
biochemically (Figure 3) and radiologically (Figure 1d). Aside from treatment for
neutropenic sepsis following the third cycle, the patient was able to complete six
cycles of chemotherapy.
Tumours with mutations in genes involving homologous recombination such as
BRCA2 are sensitive to PARP inhibition, with a recent phase II study
demonstrating biochemical, radiological and survival benefits in patients with
BRCA2-mutant prostate cancer (Mateo et al., 2015, McCabe et al., 2006). After
completion of chemotherapy, the patient was started on the PARP inhibitor
rucaparib, which was generously provided by Clovis Oncology for use on a
compassionate basis outside of a clinical trial. The patient continues on
rucaparib with clinical benefit at the time of submission (13 months).
Discussion
This case highlights the potential value of re-biopsy and utility of WGS in
personalised treatment of prostate cancer. The further biopsy of the rib lesion
was performed in the face of progressive disease despite falling PSA levels,
revealing a BRACA2 deletion not present in the germline. To our knowledge, this
is the first case study demonstrating the identification of a BRCA2 deletion in
dedifferentiated prostate cancer.
The dedifferentiation of cancers from adenocarcinoma to small cell carcinoma is
more commonly observed in EGFR mutated lung cancer and may confer
sensitivity to platinum based therapies (Sequist LV et al., 2011). Such
dedifferentiation with small cell recurrence has similarly been described in
breast adenocarcinoma in a germline BRCA2 mutation carrier (Niravath P et al., Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
2015). The induction of neuroendocrine transformation in adenocarcinoma of
the prostate is recognised and is associated with loss of tumour suppressor
genes (such as TP53 which was mutated in this case), loss of androgen-related
pathways and activation of mitotic pathways such as Aurora Kinase A thought to
play significant roles (Li Z et al., 2013, Vlachostergios PJ and Papandreou CN,
2015). Typically this transformation is thought to occur after a more prolonged
duration of androgen deprivation than reported here (Beltran H et al., 2012).
New guidelines regarding the immunohistochemical classification of small cell
carcinoma of the prostate emphasise the need for accurate classification of this
aggressive subtype of prostate cancer, which is known to be particularly
platinum sensitive (Epstein JI et al., 2014 ).
WGS of the rib lesion found a homozygous deletion of BRCA2 leading to
successful treatment with a PARP inhibitor. It is important to note that, despite
the family history, this patient was not found to carry a known pathogenic BRCA1
or BRCA2 mutation and this observation was only made through sequencing
tumoural DNA. WGS promises to offer a new level of personalised therapy; as
illustrated here and in other cases such as the recent use of WGS to identify BCL2
inhibitors as a therapeutic option for a patient with Chronic Myeloid Leukaemia
(CML) resistant to ponatinib therapy (Korfi K et al., 2015). Here we demonstrate
that adoption of a lower threshold for repeat biopsy and consideration of WGS
can have a significant and beneficial impact on patient treatment and outcomes.
Whilst we would not advocate repeat biopsies and sequencing for all patients,
our report suggests this may be particularly pertinent in cases with rapid
progression on standard treatment or an unusual clinical phenotype. This study, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
amongst others, supports the notion that as the costs of WGS falls, clinicians
should increasingly consider this approach as it may reveal avenues to
personalised cancer treatment.
Methods
DNA Extraction
Germline DNA was isolated from 1.5 mL peripheral blood using the
QIASymphony DSP DNA Midi kit (Qiagen), according to the manufacturer’s
protocol. Tumour DNA was extracted from fresh frozen tissue using the All Prep
Mini DNA Extraction kit (Qiagen), as described in the manufacturer’s protocol.
Library Preparation and Whole Genome Sequencing
Libraries of 350 bp fragments were generated from 1 µg sheared genomic DNA
using the TruSeq PCR-Free library preparation kit (Illumina, San Diego, CA).
2x126 paired-end sequencing was performed using the HiSeq2500 HTv4.
(Illumina, San Diego, CA). Whole genome sequencing was performed at a
coverage of 30x for the germline and of 75x for the tumour (Supplementary
Table S1).
Bioinformatic Data Analysis - SNV calling
Paired-end alignment of sequencing data against the reference genome hg19
(GRCh 37) was performed using the Whole Genome Sequencing Application v2.0,
based on Isaac Alignment Tool (Raczy et al., 2013), within BaseSpace, a cloud-
based analysis tool suit (Illumina, San Diego, CA). Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Somatic single nucleotide (SNV) and insertion/deletion (InDels) variant calling
analysis was performed using the Tumour-Normal Application v1.0, based on
Strelka (Saunders et al., 2012), within BaseSpace. Calls were annotated using the
variant effect predictor v2.8 (McLaren et al., 2016), COSMIC v77 (Forbes et al.,
2015) and 1000 Genomes v3 (1000 Genomes Project Consortium, 2015). The
SIFT (Kumar et al., 2009) and PolyPhen-2 (Adzhubei et al., 2010) algorithms
were used to evaluate the impact of a mutation on protein structure or function
as predicted by Ensembl (v84) (McLaren et al., 2016). All variants of interest
were manually inspected using integrative genomics viewer (IGV) (Robinson et
al., 2011).
Copy Number Analysis - Structural variants and translocations detection
Structural variant (SV) calling analysis was performed locally using BreakDancer
[v1.4.5] (Chen et al., 2009). Analysis was limited to a set of disease specific genes,
as defined in Atlas of Genetics and Cytogenetics in Oncology and Haematology
(Huret et al., 2013), accessed at the time of analysis.
The coverage of the aligned sequence data was determined by the total number
of aligned bases divided by the genome size. This information is provided by the
Whole Genome Sequencing Application v2.0 (Raczy et al., 2013).
Manual inspection in IGV is essential for each of the translocations reported by
BreakDancer in order to view the complexity and quality of the sequence
alignment of the regions that were reported and to verify whether the event is
somatic or germline.
Clinical Interpretation Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
All SNVs, InDels and CNVs identified within the COSMIC Cancer Genes Census
(v77) (Forbes et al., 2015) ranked with respect to their pathogenicity and clinical
actionability (Futreal et al, 2004). A number of different sources, including
COSMIC (Forbes et al., 2015), ‘MyCancerGenome’ (www.mycancergenome.org)
and ClinicalTrials.gov (www.clinicaltrials.gov) were used to determine whether
genetic alterations were clinically relevant.
Table 1 and Supplementary Table S2 contain details of this analysis.
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Additional Details
Data Deposition and Access
Details of specific variants are deposited in the ClinVar database
(http://www.ncbi.nlm.nih.gov/clinvar/) under Accession Numbers
SCV000493831 (BRCA2), SCV000493830 (PTEN) and SCV000493829 (TP53).
Ethics Statement
Written consent for this case study, sequencing and publication thereof was
obtained and ethical approval granted in line with the BRC Cancer Pilot (Ref:
14/SC/1165 South Central Berkshire B REC) Written consent did not include
WGS archiving or raw data deposition.
Acknowledgements
We thank the patient for his involvement and agreement to us sharing this case.
Author Contributions
KP and BPF wrote and revised the manuscript and KP created the table and
figures. AS, SK, PA, HD, NP and JT performed the WGS and subsequent analysis.
AP edited the manuscript and was involved in the clinical management of the
patient. IR, LB, ZT, DK, CV, KG and MT were involved in the clinical diagnosis and
management of the patient.
Funding Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
This study was funded by the Wellcome Trust and Department of Health as part
of the Health Innovation Challenge Fund. The views expressed in this
manuscript are those of the authors and not necessarily Wellcome Trust and
Department of Health. BPF was a National Institute for Health Research (NIHR)-
funded Clinical Lecturer and is a Wellcome Trust Funded Intermediate Clinical
Fellow (ref:201488/Z/16/Z). KP is an NIHR-funded Academic Clinical Fellow.
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
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Figure Legends
Figure 1:
CT and MRI images demonstrating disease course
1a) Initial staging CT scan. Axial section of lumbar spine, soft tissue window,
demonstrating mild bone erosion (arrow) indicating bone metastasis.
b) Image at month 2.5 (see figure 3 for ALP/PSA correlation) - MRI spine,
axial section, demonstrating L4 lesion invading into right pedicle
c) Image at month 4 – MRI spine, axial section, demonstrating further
increase in L4 lesion with extensive metastatic marrow infiltration.
d) Image at month 10.5 – CT scan, bone window, demonstrating significant
reduction in the lesion at L4.
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Figure 2
2a, 2b – Prostatic biopsies on diagnosis stained with haematoxylin and eosin
(H&E) right (2a - Gleason Score 8 (4+4)) and left (2b – Gleason Score 7 (4+3))
sided infiltration by acinar type prostatic adenocarcinoma. Fig 2b shows areas of
large cribriform Gleason pattern 4 adenocarcinoma (the absence of basal cells
was confirmed with immunohistochemistry).
2c, 2d: Rib biopsy during disease progression stained with H&E (2c) and
immunohistochemical staining (2d). Figure 2c shows areas of necrosis with
hyperchromatic nuclei and little cytoplasm. In figure 2d, whilst staining for
neuroendocrine markers CD56 (NCAM), Synaptophysin and Chromogranin A
was negative, TTF-1 showed very focal nuclear positivity (arrow). Pan
Cytokeratin staining showed diffuse membrane positivity and PSA (polyclonal)
staining was negative. The features were of metastatic carcinoma and, in view of
the morphology, favoured small cell carcinoma.
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Figure 3
Timeline of Prostate Specific Antigen (PSA) and Alkaline Phosphatase (ALP)
levels and management interventions from diagnosis
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Figure 4
Log R plots generated using WGS read count information from tumour versus
germline data:
a) Large regions of acquired CN Loss involving chr13 are identified in the
tumour sample together with a ~1.68Mb region of acquired homozygous loss
encompassing the BRCA2 gene (highlighted respectively by the single and double
red bars below the ideogram);
b) enlarged image of the acquired homozygous loss encompassing BRCA2.
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Table 1: Mutation analysis of tumour genetic sequence. * indicates these are recognised mutations in primary prostate cancer. (Cancer Genome Atlas Research Network, 2015)
Gene mutation Mutation Chromosome Start Finish CDC73 CN gain 1 170,479,674 198,492,877 VHL CN gain 3 0 16,153,088 PDGFRA CN gain 4 52,652,733 65,798,728 C-KIT CN gain 4 52,652,733 65,798,728 NFKB CN loss 4 65,798,728 191,154,276 FBXW7 CN loss 4 65,798,728 191,154,276 PIK3R * CN loss 5 49,405,693 97,198,579 APC CN loss 5 101,904,635 130,674,136 JAK2 CN loss 9 64,626 10,139,240 CDKN2A CN gain 9 10,320,113 26,205,565 PTCH1 CN gain 9 73,037,883 112,950,586 NOTCH1 CN gain 9 134,275,097 141,213,431 PTEN * CN loss 10 85,557,432 105,804,295 HRAS CN loss 11 0 11,638,440 WT1 CN gain 11 29,272,732 34,694,617 KRAS CN loss 12 8,485,813 32,425,114 FLT3 CN loss 13 19,020,013 32,178,877 BRCA2 Homozygous copy 13 32,178,877 33,860,144 loss RB1 CN loss 13 33,860,144 109,025,409 CDH1 CN loss 16 46,455,960 90,354,753 TP53 * CN loss 17 7,506,837 7,671,804 PAK7 CN loss 20 0 14,782,559
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Table 2: Variant Table - Summary of BRCA2 mutation
Gene Chromo- HGVS DNA HGVS Variant Predicted dbSNP/dbVar Genotype some Reference Protein Type Effect ID Reference BRCA2 13 g. 32178877- n/a Copy Loss of n/a Homozygous 33860144del loss function
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Supplementary Table S1 - Whole Genome Sequencing (WGS) coverage and mapped reads
• Germline – WGS Average Coverage: 27.40x
General Information Total Reads Mapped Reads % Mapped Properly Paired % Properly Paired reads Reads Reads 722,500,052 690,234,773 95.3 665,067,106 92.0
Coverage Information over the Whole Exome Average Coverage % Bases above 10x % Bases above 20x % Bases above 30x 28.12x 98.2 86.5 42.7
• Tumour – WGS Average Coverage: 85.44x
General Information Total Reads Mapped Reads % Mapped Properly Paired % Properly Paired reads Reads Reads 2,278,844,976 2,185,930,417 95.92 2,084,723,948 91.48
Coverage Information over the Whole Exome Average Coverage % Bases above 10x % Bases above 20x % Bases above 30x 89.5 99.2 98.8 98.2
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Supplementary Table S2 - Summary of mutations identified by WGS
Chr Start End Acquired Length (bp) Cytoband Gene Symbols OncoScan SomMut Markers Event 1 0 26,138,050 CN Loss 26138051 p36.33 - p36.11 DDX11L1, MIR6859-1, MIR6859-2, 0 WASH7P, FAM138A, FAM138F, OR4F5, LOC729737, DQ597235, DQ599768, LOC100133331, LOC100132062, LOC100132287, LOC388312, OR4F16, OR4F29, BC036251, JA429830, JA429831, JB137814, MIR6723, M37726, OR4F29, OR4F3, DQ575786, DQ599872, LOC100133331, AK310751, LOC100288069, FAM87B, LINC00115, LINC01128, LOC643837, FAM41C, AK056486, LOC100130417, SAMD11, NOC2L, KLHL17, PLEKHN1, C1orf170, PERM1, HES4, ISG15, AGRN, AK310350, BC033949, RNF223, C1orf159, LOC254099, MIR200B, MIR200A, JA715134, MIR429, JA715143, AK128833, TTLL10, TNFRSF18, TNFRSF4, SDF4, SDF4, B3GALT6, FAM132A, UBE2J2, SCNN1D, MIR6726, ACAP3, PUSL1, MIR6727, CPSF3L, GLTPD1, TAS1R3, MIR6808, DVL1, MXRA8, AURKAIP1, CCNL2, LOC148413, MRPL20, ANKRD65, TMEM88B, VWA1, ATAD3C, ATAD3B, ATAD3A, AX747755, TMEM240, SSU72, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
1 27,148,195 28,578,367 CN Loss 1430173 p36.11 - p35.3 ZDHHC18, SFN, GPN2, GPATCH3, 0 NR0B2, NUDC, BC016143, KDF1, C1orf172, TRNP1, FAM46B, SLC9A1, DL490887, WDTC1, LOC644961, TMEM222, SYTL1, MAP3K6, FCN3, CD164L2, GPR3, WASF2, AHDC1, FGR, IFI6, FAM76A, STX12, SCARNA1, PPP1R8, THEMIS2, RPA2, SMPDL3B, XKR8, EYA3, PTAFR, DNAJC8, ATPIF1, JA611241 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
1 170,479,674 198,492,877 CN Gain 28013204 q24.2 - q31.3 AK096329, GORAB, PRRX1, MROH9, CDC73_pW43X_c128G_A MIR1295A, MIR1295B, FMO3, FMO6P, FMO2, FMO1, FMO4, TOP1P1, PRRC2C, MYOC, VAMP4, METTL13, AK094818, DNM3, MIR3120, MIR214, DNM3OS, MIR199A2, PIGC, C1orf105, SUCO, FASLG, TNFSF18, TNFSF4, LOC100506023, BC136808, PRDX6, SLC9C2, LOC730159, ANKRD45, KLHL20, CENPL, DARS2, GAS5-AS1, SNORD81, SNORD47, SNORD80, SNORD79, SNORD78, GAS5, SNORD44, SNORD77, SNORD76, SNORD75, SNORD74, ZBTB37, DQ593451, SERPINC1, RC3H1, GPR52, RABGAP1L, CACYBP, MRPS14, TNN, KIAA0040, TNR, AK093214, BC043291, SCARNA3, RFWD2, PAPPA2, AK096718, ASTN1, MIR488, FAM5B, BRINP2, LOC101928778, SEC16B, LOC730102, RASAL2-AS1, RASAL2, TEX35, C1orf220, MIR4424, RALGPS2, ANGPTL1, FAM20B, TOR3A, ABL2, DD413682, SOAT1, AXDND1, NPHS2, DQ592690, DQ571986, DQ600552, DQ595741, DQ601755, DQ592269, DQ577099, DQ587855, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
1 198,492,878 230,986,905 High Copy 32494028 q31.3 - q42.2 ATP6V1G3, PTPRC, MIR181B1, 0 Gain MIR181A1, MIR181A1HG, LINC01222, BC040869, NR5A2, LINC00862, ZNF281, EU250746, KIF14, DDX59, LOC101929224, CAMSAP2, GPR25, C1orf106, C1orf81, KIF21B, BC016656, CACNA1S, ASCL5, TMEM9, IGFN1, PKP1, AK055533, TNNT2, TNNT2, LAD1, TNNI1, PHLDA3, CSRP1, RPS10P7, AX747377, MIR5191, NAV1, IPO9-AS1, RNU6-79P, MIR1231, IPO9, MIR6739, SHISA4, LMOD1, TIMM17A, RNPEP, MIR6740, ELF3, GPR37L1, ARL8A, PTPN7, PTPRVP, LGR6, UBE2T, PPP1R12B, SYT2, KDM5B, PCAT6, KDM5B-AS1, LOC641515, BC040684, BC049825, LOC148709, RABIF, KLHL12, ADIPOR1, CYB5R1, LOC401980, LOC100506747, TMEM183B, TMEM183A, PPFIA4, MYOG, ADORA1, MYBPH, BC034684, CHI3L1, CHIT1, LOC100506775, LINC01136, LOC730227, BTG2, FMOD, PRELP, OPTC, ATP2B4, U42379, SNORA77, LINC00260, LAX1, ZBED6, ZC3H11A, SNRPE, LINC00303, SOX13, ETNK2, BC038769, REN, KISS1, GOLT1A, PLEKHA6, PLEKHA6, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
1 230,986,906 241,946,332 CN Gain 10959427 q42.2 - q43 C1orf198, LOC101927604, BC032911, 0 TTC13, ARV1, MIR1182, FAM89A, LOC149373, TRIM67, C1orf131, GNPAT, EXOC8, SPRTN, EGLN1, SNRPD2P2, TSNAX, LINC00582, TSNAX- DISC1, DISC2, DISC1, SIPA1L2, LOC101927683, MAP10, NTPCR, PCNXL2, KIAA1804, MIR4427, KCNK1, SLC35F3, AK054726, MIR4671, COA6, TARBP1, LOC100506795, IRF2BP2, LINC00184, BC032040, LINC01132, LOC100506810, BC016972, TOMM20, SNORA14B, RBM34, MIR4753, ARID4B, GGPS1, TBCE, B3GALNT2, AX747026, GNG4, LYST, MIR1537, NID1, AX747246, GPR137B, ERO1LB, EDARADD, LGALS8-AS1, LGALS8, HEATR1, ACTN2, MTR, MT1HL1, RYR2, ZP4, LOC100130331, LINC01139, LOC339535, CHRM3, CHRM3-AS2, CHRM3-AS1, RPS7P5, FMN2, GREM2, RGS7, MIR3123, FH, KMO, OPN3, CHML, WDR64
1 241,946,333 242,628,315 cnLOH 681983 q43 WDR64, EXO1, BECN1P1, MAP1LC3C, 0 PLD5 1 242,628,316 244,221,452 CN Gain 1593137 q43 - q44 PLD5, LOC731275, Mir_350, CEP170, 0 MIR4677, SDCCAG8, AKT3, LOC339529, ZBTB18, AK310634 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
1 244,221,453 244,423,458 High Copy 202006 q44 0 0 Gain 2 14,057,047 14,076,539 CN Loss 19493 p24.3 0 0 2 103,694,579 103,752,839 CN Loss 58261 q12.1 0 0 2 103,909,636 104,084,950 CN Loss 175315 q12.1 0 0 2 104,172,062 168,223,828 CN Loss 64051767 q12.1 - q24.3 LOC100287010, LINC01102, 0 LOC150568, LINC01103, LINC01114, LOC284998, LINC01158, LOC100506421, POU3F3, AK095498, LINC01159, LOC102724691, MRPS9, LOC101927492, GPR45, LOC644617, TGFBRAP1, C2orf49, FHL2, LOC285000, NCK2, C2orf40, UXS1, PLGLA, RGPD3, ST6GAL2, RGPD4-AS1, LOC729121, RGPD4, SLC5A7, SULT1C3, SULT1C2, SULT1C2P1, SULT1C4, GCC2, FLJ38668, LIMS1, RANBP2, CCDC138, EDAR, SH3RF3- AS1, MIR4265, MIR4266, SH3RF3, SEPT10, AX747172, SOWAHC, RGPD5, RGPD6, LIMS3L, LIMS3, LIMS3- LOC440895, LOC440895, LOC100288570, DQ584199, LINC01123, LOC440894, MIR4267, MIR4436B1, MIR4436B2, MALL, NPHP1, LINC00116, LOC100507334, DQ595602, DQ587734, MIR4436B1, LINC01106, LOC151009, LINC01123, DQ586666, DQ581602, LOC440895, LIMS3-LOC440895, LIMS3L, RGPD5, BUB1, DQ594093, DQ573754, DQ593945, DQ574014, DQ592678, 2 235,595,691 235,675,218 CN Gain 79528 q37.1 - q37.2 DQ599706, DQ586378, DQ573409, 0 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
3 0 16,153,088 CN Gain 16153089 p26.3 - p25.1 LOC102723448, CHL1, CHL1-AS1, VHL_p_c463_plus_2T_C, BC065754, AK126307, LINC01266, VHL_p_c464_minus_1G_A, CNTN6, CNTN4-AS2, CNTN4, IL5RA, VHL_pP61P_c183C_T, TRNT1, CRBN, BC141932, LRRN1, VHL_pS65L_c194C_T, SUMF1, SETMAR, ITPR1-AS1, ITPR1, VHL_pS68X_c203C_A, EGOT, BHLHE40-AS1, BHLHE40, VHL_pP81S_c241C_T, ARL8B, EDEM1, MIR4790, VHL_pL85P_c254T_C, Metazoa_SRP, AF279782, VHL_pW88X_c263G_A, LOC101927347, GRM7, VHL_pQ96X_c286C_T, LOC101927394, AK124857, LMCD1- VHL_pG114C_c340G_T, AS1, U4atac, LMCD1, DQ591848, VHL_pH115Y_c343C_T, LINC00312, AX747864, SSUH2, CAV3, VHL_pW117R_c349T_C, OXTR, Mir_548, RAD18, SRGAP3, VHL_pW117X_c350G_A, BC041457, SRGAP3-AS3, SETD5-AS1, VHL_pL118P_c353T_C, THUMPD3, THUMPD3-AS1, SETD5, VHL_pQ132X_c394C_T, LHFPL4, MTMR14, CPNE9, BRPF1, VHL_pI151S_c452T_G, OGG1, AX748417, CAMK1, TADA3, VHL_pL153P_c458T_C, ARPC4, TTLL3, ARPC4-TTLL3, RPUSD3, VHL_p_c463_plus_1G_T, JAGN1, IL17RE, IL17RC, CRELD1, VHL_pE160K_c478G_A, CIDEC, PRRT3, PRRT3-AS1, EMC3, VHL_pR161X_c481C_T, AX747493, AK125558, EMC3-AS1, VHL_pR167W_c499C_T, LOC401052, FW339974, CIDECP, VHL_pS183X_c548C_A, FANCD2, FANCD2OS, BRK1, VHL, VHL_pL184P_c551T_C, IRAK2, TATDN2, LINC00852, GHRLOS, VHL_pE189K_c565G_A GHRL, SEC13, MIR885, ATP2B2, LINC00606, SLC6A11, SLC6A1-AS1, SLC6A1, HRH1, ATG7, AX748267, 3 125,714,676 125,818,900 CN Gain 104225 q21.2 - q21.3 SLC41A3VGLL4, TAMM41, DQ583118, SYN2, 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
3 125,818,900 127,636,899 High Copy 1818000 q21.3 SLC41A3, ALDH1L1-AS1, ALDH1L1, 0 Gain ALDH1L1-AS2, KLF15, BC033989, CCDC37-AS1, CCDC37, UNQ2790, ZXDC, UROC1, CHST13, C3orf22, TXNRD3NB, TXNRD3, NUP210P1, CHCHD6, PLXNA1, C3orf56, LOC101927123, BC015846, BX537548, MIR6825, TPRA1, MCM2, PODXL2, ABTB1, MGLL, KBTBD12
3 127,636,900 128,042,606 CN Loss 405707 q21.3 KBTBD12, SEC61A1, RUVBL1, EEFSEC 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
4 52,652,733 65,798,728 CN Gain - 13145996 q11 - q13.1 DCUN1D4, LRRC66, SGCB, SPATA18, PDGFRA_pN659K_c1977C_A, includes USP46, MIR4449, DANCR, SNORA26, PDGFRA_pT674I_c2021C_T, REST ERVMER34-1, LOC152578, RASL11B, PDGFRA_pF808L_c2422T_C, BC042091, AK055055, SCFD2, FIP1L1, PDGFRA_pV824V_c2472C_T, LNX1-AS1, LNX1, LNX1-AS2, PDGFRA, PDGFRA_pD842Y_c2524G_T, RPL21P44, CHIC2, GSX2, BC044946, PDGFRA_pD842V_c2525A_T_allele1, KIT, DL490879, KDR, Metazoa_SRP, PDGFRA_pD846Y_c2536G_T, SRD5A3, SRD5A3-AS1, TMEM165, PDGFRA_pN870S_c2609A_G, CLOCK, PDCL2, NMU, U6, LOC644145, PDGFRA_pD1071N_c3211G_A, EXOC1, CEP135, KIAA1211, AASDH, KIT_pV560D_c1679T_A_allele1, PPAT, PAICS, SRP72, ARL9, THEGL, KIT_pL576P_c1727T_C, Mir_720, HOPX, SPINK2, REST, NOA1, KIT_pF584S_c1751T_C, POLR2B, IGFBP7, LOC255130, IGFBP7- KIT_pD52N_c154G_A, AS1, BC034799, LPHN3, Y_RNA, KIT_pY503_F504insAY_c1509_1510insGC BC039452, LOC101927186, TECRL, CTAT_allele1, LOC401134 KIT_pW557_K558del_c1669_1674delTG GAAG_allele1, KIT_pW557R_c1669T_C, KIT_pV559A_c1676T_C, KIT_pP585P_c1755C_T, KIT_pK642E_c1924A_G, KIT_pV654A_c1961T_C, KIT_pT670I_c2009C_T, KIT_pI798I_c2394C_T, KIT_pD816Y_c2446G_T, KIT_pN822K_c2466T_G, KIT_pY823D_c2467T_G, KIT_pV825A_c2474T_C, KIT_pE839K_c2515G_A Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
4 65,798,728 191,154,276 CN Loss 125355549 q13.1 - q35.2 LOC401134, EPHA5, LOC100144602, NFKB1_p_c40_minus_1G_A, TRNA, LOC101927237, AK093203, FBXW7_pS582L_c1745C_T, CENPC, CENPC1, STAP1, UBA6, UBA6- FBXW7_pR505C_c1513C_T, AS1, BC045560, GNRHR, TMPRSS11D, FBXW7_pR479Q_c1436G_A, LOC550112, TMPRSS11A, FBXW7_pR465H_c1394G_A, TMPRSS11GP, SYT14L, LOC550113, FBXW7_pR465C_c1393C_T, TMPRSS11F, FTLP10, TMPRSS11BNL, FBXW7_pR393X_c1177C_T, TMPRSS11B, YTHDC1, TMPRSS11E, FBXW7_pR278X_c832C_T, UGT2B17, UGT2B15, UGT2B10, FBXW7_pR224X_c670C_T UGT2A3, UGT2B7, UGT2B11, AK124272, UGT2B28, UGT2B4, UGT2A2, UGT2A1, SULT1B1, SULT1E1, CSN1S1, CSN2, STATH, HTN3, HTN1, CSN1S2AP, CSN1S2BP, C4orf40, PRR27, ODAM, FDCSP, CSN3, CABS1, SMR3A, SMR3B, PROL1, MUC7, AMTN, AMBN, ENAM, IGJ, UTP3, RUFY3, GRSF1, MOB1B, DCK, SLC4A4, GC, NPFFR2, ADAMTS3, COX18, ANKRD17, ALB, AFP, AFM, LOC728040, RASSF6, IL8, CXCL8, CXCL6, PF4V1, CXCL1, PF4, PPBP, CXCL5, CXCL3, PPBPP2, CXCL2, LOC541467, MTHFD2L, BC016361, EPGN, EREG, AREG, BTC, AK027257, PARM1, LOC441025, RCHY1, THAP6, C4orf26, CDKL2, G3BP2, AK311578, USO1, PPEF2, NAAA, SDAD1, CXCL9, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
5 1 46,427,438 cnLOH 46427438 p15.33 - p11 PLEKHG4B, LRRC14B, CCDC127, SDHA, 0 LOC102467073, PDCD6, AHRR, C5orf55, EXOC3, FLJ00157, AK023178, PP7080, BC013821, SLC9A3, MIR4456, LOC100996325, CEP72, TPPP, ZDHHC11, BRD9, TRIP13, LOC100506688, NKD2, MIR4635, SLC12A7, CTD-3080P12.3, BC032469, SLC6A19, SLC6A18, TERT, MIR4457, AK126225, CLPTM1L, DQ598099, BC034612, SLC6A3, LPCAT1, MIR6075, CR749689, SDHAP3, LOC728613, MIR4277, MRPL36, NDUFS6, LOC101929034, IRX4, CTD- 2194D22.4, MIR548BA, LOC100506858, IRX2, C5orf38, LOC102467074, LINC01019, LOC285577, LOC102467075, IRX1, LOC101929153, BC034630, LINC01020, LOC340094, AK094462, CTD-2297D10.2, ADAMTS16, KIAA0947, FLJ33360, MED10, UBE2QL1, LINC01018, LOC255167, NSUN2, SRD5A1, LOC100505625, PAPD7, MIR4278, MIR4454, LOC442132, ADCY2, C5orf49, FASTKD3, MTRR, LOC729506, MIR4458HG, LOC100505738, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
5 49,405,693 97,198,579 CN Loss 47792887 q11.1 - q15 EMB, PARP8, LOC100287592, PIK3R1_pG376R_c1126G_A LOC642366, ISL1, PELO, ITGA1, AK097288, ITGA2, MOCS2, LOC257396, FST, NDUFS4, BC048141, MIR581, Metazoa_SRP, ARL15, HSPB3, SNX18, LOC102467080, ESM1, LOC102467081, GZMK, Y_RNA, GZMA, CDC20B, GPX8, MIR449A, MIR449B, MIR449C, MCIDAS, CCNO, DHX29, SKIV2L2, PPAP2A, MIR5687, RNF138P1, SLC38A9, DDX4, IL31RA, IL6ST, FLJ31104, U6, ANKRD55, U6atac, LOC102467147, LOC101928448, MAP3K1, SETD9, MIER3, GPBP1, ACTBL2, LOC101928505, LOC101928539, LOC101928569, Mir_562, PLK2, GAPT, LOC101928600, RAB3C, AB074188, BX641110, Mir_582, PDE4D, PART1, DEPDC1B, ELOVL7, ERCC8, NDUFAF2, SMIM15, CTC-436P18.1, ZSWIM6, BC032910, C5orf64, BC043229, BC043516, LOC101928651, BC043261, BC039381, LOC100506526, KIF2A, DIMT1, IPO11, LRRC70, IPO11-LRRC70, HTR1A, RNF180, RGS7BP, FAM159B, 5 97,198,579 101,904,635 Homozygou 4706057 q15 - q21.1 HM358988,SREK1IP1, Mir_340, RGMB-AS1, CWC27, RGMB, CHD1, 0 s Copy Loss LOC100289230, DQ597441, CTD- 2151A2.1, JB137812, LOC100133050, DQ583509, FAM174A, ST8SIA4, SLCO4C1, SLCO6A1 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
5 101,904,635 130,674,136 CN Loss 28769502 q21.1 - q31.1 LINC00492, AX747345, LINC00491, APC_pR213X_c637C_T, PAM, GIN1, PPIP5K2, C5orf30, APC_pR232X_c694C_T, LOC102467212, NUDT12, RAB9BP1, APC_p_c835_minus_8A_G, LOC102467213, EFNA5, FBXL17, APC_pR283X_c847C_T, LINC01023, HP07349, BC034788, FER, APC_pR302X_c904C_T, AK021888, JB023059, PJA2, MAN2A1, APC_pR332X_c994C_T, LOC100289673, TMEM232, SNORA51, APC_pR564X_c1690C_T, SLC25A46, TSLP, WDR36, CAMK4, APC_pQ789X_c2365C_T, STARD4, STARD4-AS1, NREP, NREP- APC_pE853X_c2557G_T, AS1, EPB41L4A-AS1, SNORA13, APC_pR876X_c2626C_T, LOC101927023, EPB41L4A, FLJ11235, APC_pR1114X_c3340C_T, EPB41L4A-AS2, LOC102467214, APC_pS1281X_c3842C_A, LOC102467216, APC, SRP19, ZRSR1, APC_pE1286X_c3856G_T, REEP5, DCP2, MCC, FLJ43978, TSSK1B, APC_pQ1291X_c3871C_T, U4atac, YTHDC2, KCNN2, AK097686, APC_pQ1294X_c3880C_T, TRIM36, PGGT1B, CCDC112, FEM1C, APC_pE1309fs4_c3921_3925delAAAAG_ TICAM2, TMED7-TICAM2, allele1, LOC101927100, TMED7, APC_pE1309fs6_c3923_3924insA_allele1 LOC102467217, CDO1, ATG12, AP3S1, , APC_pE1309X_c3925G_T, AX747550, AQPEP, ARL14EPL, APC_pE1309fs4_c3927_3931delAAAGA_ COMMD10, LOC101927190, CTB- allele1, APC_pE1322X_c3964G_T, 118N6.3, SEMA6A, Mir_633, APC_pQ1328X_c3982C_T, LOC102467223, LINC00992, APC_pQ1338X_c4012C_T, LOC728342, LOC102467224, APC_pS1341R_c4023T_G, BC044609, LOC100505811, APC_pE1345X_c4033G_T, LOC101927280, LOC102467225, APC_pE1353X_c4057G_T, DTWD2, MIR1244-1, MIR1244-2, APC_pQ1367X_c4099C_T, 6 57,202,434 58,140,638 CN Loss 938205 p11.2 PRIM2MIR1244-3, BC036311, DMXL1, APC_pQ1378X_c4132C_T, 0 6 61,880,946 63,017,763 CN Loss 1136818 q11.1 MTRNR2L9, KHDRBS2 0 6 70,162,067 70,188,348 CN Loss 26282 q13 0 0 6 72,089,455 72,104,503 CN Loss 15049 q13 0 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
6 72,890,949 74,093,387 CN Loss 1202439 q13 RIMS1, KCNQ5-IT1, KCNQ5, MIR4282, 0 KCNQ5-AS1, KHDC1L, KHDC1, BC031876, AL832252, C6orf147, DPPA5, KHDC3L, OOEP 6 74,417,601 75,787,443 CN Loss 1369843 q13 CD109, LOC101928516, AF086303 0 6 75,896,327 75,965,932 CN Loss 69606 q13 - q14.1 COL12A1, COX7A2, TMEM30A 0 6 76,195,729 77,436,689 CN Loss 1240961 q14.1 FILIP1, SENP6, MYO6, IMPG1 0 6 77,456,848 78,940,754 CN Loss 1483907 q14.1 HTR1B, MEI4 0 6 90,314,978 90,348,595 CN Loss 33618 q15 ANKRD6, LYRM2, LOC101929057 0 6 96,666,569 103,740,578 CN Gain 7074010 q16.1 - q16.3 UFL1, FHL5, U4, GPR63, NDUFAF4, 0 Metazoa_SRP, KLHL32, MMS22L, MIR548H3, AK091365, LOC101927314, MIR2113, POU3F2, FBXL4, FAXC, COQ3, BC033061, PNISR, DQ599242, USP45, TSTD3, CCNC, PRDM13, MCHR2, MCHR2-AS1, LOC728012, SIM1, ASCC3, DQ585302, GRIK2 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
6 103,762,789 118,438,903 CN Gain 14676115 q16.3 - q22.2 HACE1, LINC00577, LIN28B, BVES, 0 BVES-AS1, POPDC3, PREP, PRDM1, ATG5, AIM1, RTN4IP1, QRSL1, LOC100422737, AK123416, C6orf203, BEND3, PDSS2, SOBP, SCML4, SEC63, AJ420489, OSTM1, AF520419, NR2E1, SNX3, LACE1, FOXO3, LINC00222, ARMC2, ARMC2-AS1, SESN1, CEP57L1, LOC100996634, CCDC162P, C6orf185, CD164, PPIL6, SMPD2, MICAL1, ZBTB24, AK9, AK9, FIG4, GPR6, WASF1, CDC40, METTL24, DDO, SLC22A16, CDK19, BC047513, AMD1, GTF3C6, RPF2, GSTM2P1, SLC16A10, KIAA1919, REV3L, AF216583, TRAF3IP2-AS1, TRAF3IP2, FYN, WISP3, TUBE1, FAM229B, LAMA4, RFPL4B, MARCKS, LINC01268, LOC285758, FLJ34503, HDAC2, BC042098, Mir_320, HS3ST5, Mir_548, Mir_584, FRK, TPI1P3, COL10A1, NT5DC1, TSPYL4, AK093256, TSPYL1, DSE, FAM26F, FAM26E, TRAPPC3L, FAM26D, RWDD1, RSPH4A, ZUFSP, AX746765, KPNA5, FAM162B, GPRC6A, RFX6, VGLL2, ROS1, GOPC, DCBLD1, 6 118,489,760 119,286,553 CN Gain 796794 q22.2 - q22.31 SLC35F1,AJ420595, BRD7P3, LOC101927919, PLN, CEP85L, NUS1, 0 LOC100287632, MCM9, ASF1A, FAM184A 6 119,321,071 120,141,501 CN Gain 820431 q22.31 FAM184A, MIR548B, MAN1A1, 0 LOC285762 6 120,157,874 120,358,108 CN Gain 200235 q22.31 0 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
6 120,369,437 120,929,676 CN Gain 560240 q22.31 0 0 7 27,961,464 37,358,056 CN Loss 9396593 p15.2 - p14.1 JAZF1, U6, JAZF1-AS1, BC087859, 0 CREB5, TRIL, DQ601810, LOC100506497, CPVL, LOC101928168, LOC102724484, CHN2, Mir_340, BC038570, PRR15, BC121815, LOC646762, MIR550A3, ZNRF2P2, DPY19L2P3, WIPF3, SCRN1, FKBP14, PLEKHA8, MTURN, C7orf41, AK098769, MIR550A1, MIR550B1, ZNRF2, DKFZP586I1420, LINC01176, NOD1, GGCT, LOC401320, AL137445, DJ031144, GARS, CRHR2, INMT, INMT- FAM188B, FAM188B, AQP1, GHRHR, ADCYAP1R1, NEUROD6, CCDC129, PPP1R17, BC043188, Mir_584, PDE1C, LOC100130673, LSM5, DPY19L1P1, ZNRF2P1, MIR550A2, MIR550B2, AK057321, LINC00997, LOC401321, AVL9, DPY19L1P2, KBTBD2, RP9P, FKBP9, AX721280, NT5C3A, DQ584906, RP9, 5S_rRNA, BBS9, hCG_1643653, AK025321, BMPER, NPSR1-AS1, NPSR1, AJ011981, DPY19L1, BC084560, DPY19L2P1, TBX20, LOC401324, HERPUD2, DQ594967, LOC100506725, LOC101928545, 7 117,729,741 117,742,473 CN Loss 12733 q31.31 SEPT7, DQ595191, LOC101928618, 0 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
8 0 24,252,431 CN Loss 24252432 p23.3 - p21.2 OR4F21, RPL23AP53, ZNF596, 0 FAM87A, FBXO25, AK056623, TDRP, C8orf42, AK128400, ERICH1, ERICH1- AS1, LOC286083, DLGAP2-AS1, DLGAP2, AK093412, CLN8, MIR596, BC047307, ARHGEF10, KBTBD11, MIR7160, MYOM2, AX747124, BC045738, AK128880, CSMD1, 7SK, LOC100287015, MCPH1, ANGPT2, MIR8055, AGPAT5, MIR4659A, MIR4659B, XKR5, LOC100652791, GS1- 24F4.2, DEFB1, DEFA6, DEFA4, DEFA8P, DEFA9P, DEFA10P, DEFA1, DEFA1B, DEFT1P, DEFT1P2, DEFA3, DEFA1B, DEFA11P, DEFA5, BC030294, FLJ00326, LINC00965, DEFB109P1B, FAM66B, USP17L1P, USP17L4, ZNF705G, DEFB4B, DEFB103A, DEFB103B, SPAG11B, DEFB104B, DEFB106A, DEFB106B, DEFB105A, DEFB105B, DEFB107A, DEFB107B, PRR23D1, PRR23D2, FAM90A7P, FAM90A10P, DEFB104A, DEFB104B, SPAG11A, DEFB103A, DEFB4A, ZNF705B, USP17L8, USP17L3, FAM66E, MIR548I3, FAM86B3P, SGK223, CLDN23, MFHAS1, ERI1, 8 30,121,907 30,138,226 CN Loss 16320 p12 MIR4660, PPP1R3B, BC017578, U6, 0 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
8 62,312,437 70,435,154 CN Gain 8122718 q12.3 - q13.2 CLVS1, ASPH, MIR4470, BC047540, 0 NKAIN3, UG0898H09, GGH, TTPA, LOC101410533, YTHDF3-AS1, YTHDF3, AK093370, LINC01289, LOC286184, LOC100130155, MIR124- 2, MIR124-2HG, BX537900, LOC401463, BHLHE22, CYP7B1, LINC00251, LINC01299, LOC286186, ARMC1, MTFR1, TRNA_Tyr, PDE7A, DNAJC5B, TRNA_Tyr, TRNA_Ala, TRIM55, CRH, LINC00967, LOC100505659, RRS1-AS1, LOC100505676, RRS1, ADHFE1, C8orf46, MYBL1, LOC645895, VCPIP1, C8orf44, C8orf44-SGK3, PTTG3P, SGK3, MCMDC2, SNORD87, SNHG6, TCF24, PPP1R42, U2, JA611241, COPS5, CSPP1, ARFGEF1, CPA6, DQ584699, BC036055, PREX2, AX747593, LOC286189, C8orf34, 5S_rRNA, LOC100505718, LOC100505739, SULF1
8 70,435,155 73,497,200 High Copy 3062046 q13.2 - q13.3 SULF1, SLCO5A1, PRDM14, NCOA2, 0 Gain LOC101926892, TRAM1, LOC286190, LACTB2, Metazoa_SRP, XKR9, EYA1, Mir_548, BC048982, MSC, LOC100132891, RNU6-83P, TRPA1, LOC392232, KCNB2 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
8 73,497,201 97,721,203 CN Gain 24224003 q13.3 - q22.1 KCNB2, LOC101926908, TERF1, 0 SBSPON, LOC100130301, RPL7, RDH10, AK128216, STAU2-AS1, STAU2, UBE2W, TCEB1, TMEM70, LY96, JPH1, GDAP1, MIR5681A, MIR5681B, FLJ39080, MIR2052, PI15, AK024242, CRISPLD1, BC062758, CASC9, HNF4G, LINC01111, ZFHX4- AS1, ZFHX4, PEX2, BC036404, PKIA, ZC2HC1A, LOC101241902, IL7, STMN2, HEY1, U7, LOC101927040, AK055332, MRPS28, TPD52, MIR5708, DJ031142, ZBTB10, Mir_562, ZNF704, PAG1, FABP5, PMP2, FABP9, FABP4, FABP12, IMPA1, SLC10A5, ZFAND1, CHMP4C, SNX16, BC038578, RALYL, LRRCC1, E2F5, AB209185, C8orf59, CA13, CA1, CA3, CA2, FW340046, REXO1L2P, REXO1L1, REXO1L1, PSKH2, ATP6V0D2, SLC7A13, BC038731, Mir_147, WWP1, RMDN1, CPNE3, CNGB3, CNBD1, DCAF4L2, DKFZp761D112, MMP16, RIPK2, OSGIN2, NBN, DECR1, CALB1, LINC00534, LINC01030, BC040572, TMEM64, NECAB1, C8orf88, LOC100127983, TMEM55A, OTUD6B- Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
8 97,721,204 133,066,762 High Copy 35345559 q22.1 - q24.22 CPQ, TSPYL5, MTDH, LAPTM4B, 0 Gain Mir_684, MATN2, RPL30, SNORA72, C8orf47, ERICH5, HRSP12, POP1, TRNA_Und, NIPAL2, KCNS2, STK3, OSR2, VPS13B, MIR599, MIR875, DL491896, COX6C, SNORD77, RGS22, FBXO43, POLR2K, SPAG1, RNF19A, MIR4471, ANKRD46, SNX31, MIR7705, PABPC1, AX746867, YWHAZ, FLJ42969, ZNF706, AK291701, NACAP1, GRHL2, NCALD, MIR5680, RRM2B, AK095151, UBR5, ODF1, KLF10, AK127183, AZIN1, ATP6V1C1, AK001351, BAALCOS, C8orf56, MIR3151, BAALC-AS1, BAALC, LOC100499183, FZD6, CTHRC1, SLC25A32, DCAF13, RIMS2, DCSTAMP, DPYS, LRP12, Mir_584, ZFPM2, OXR1, ABRA, Mir_548, ANGPT1, RSPO2, EIF3E, EMC2, TMEM74, TRHR, NUDCD1, ENY2, PKHD1L1, EBAG9, SNORD112, SYBU, AX748380, U2, KCNV1, MIR2053, CSMD3, TRPS1, LINC00536, EIF3H, UTP23, RAD21, MIR3610, RAD21-AS1, AL832163, AARD, SLC30A8, SNORA31, MED30, EXT1, AK025288, SAMD12, SAMD12-AS1, TNFRSF11B, COLEC10, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
8 133,066,763 146,364,022 CN Gain 13297260 q24.22 - q24.3 OC90, HHLA1, KCNQ3, HPYR1, LRRC6, 0 TMEM71, PHF20L1, TG, TG, MIR7848, SLA, WISP1, AX746885, NDRG1, ST3GAL1, ZFAT, ZFAT-AS1, MIR30B, MIR30D, Mir_652, LOC286094, KHDRBS3, U1, Mir_720, FAM135B, COL22A1, KCNK9, TRAPPC9, AX748239, CHRAC1, DQ574852, AGO2, Mir_28, PTK2, DENND3, SLC45A4, LINC01300, LOC731779, GPR20, AK311257, PTP4A3, MROH5, MIR4472-1, LINC00051, TSNARE1, BAI1, ARC, JH8, JRK, PSCA, AX747544, LY6K, LOC100288181, THEM6, SLURP1, LYPD2, LYNX1, LY6D, GML, CYP11B1, CYP11B2, CDC42P3, LOC100133669, LY6E, C8orf31, LY6H, GPIHBP1, ZFP41, GLI4, ZNF696, TOP1MT, RHPN1-AS1, RHPN1, MAFA, ZC3H3, GSDMD, MROH6, NAPRT1, EEF1D, BC034020, TIGD5, PYCRL, TSTA3, ZNF623, BREA2, ZNF707, CCDC166, MAPK15, FAM83H, MIR4664, FAM83H-AS1, LOC100128338, AX746851, SCRIB, MIR937, PUF60, MIR6845, NRBP2, EPPK1, MIR661, PLEC, PARP10, GRINA, SPATC1, OPLAH, MIR6846, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
9 64,626 10,139,240 CN Loss 10074615 p24.3 - p23 AY343892, AY343902, FOXD4, JAK2_pK191Q_c571A_C, CBWD1, C9orf66, DOCK8, KANK1, JAK2_pY570Y_c1710C_T, DMRT1, DMRT3, U6, LINC01230, JAK2_pV617F_c1849G_T, DMRT2, SMARCA2, FLJ35024, VLDLR- JAK2_pR683G_c2047A_G AS1, VLDLR, KCNV2, KIAA0020, Mir_548, RFX3, BC069756, GLIS3-AS1, GLIS3, Mir_320, SLC1A1, SPATA6L, PPAPDC2, CDC37L1, AK3, RCL1, MIR101-2, AK021739, JAK2, TRNA_Gln, INSL6, INSL4, RLN2, RLN1, CD274, PLGRKT, PDCD1LG2, KIAA1432, ERMP1, MLANA, KIAA2026, MIR4665, RANBP6, IL33, TPD52L3, UHRF2, GLDC, KDM4C, DQ580140, KDM4C, Mir_584, C9orf123, TMEM261, AK094342, SNORD27, Metazoa_SRP, PTPRD
9 10,139,240 10,320,113 Homozygou 180874 p23 PTPRD 0 s Copy Loss Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
9 10,320,113 26,205,565 CN Loss 15885453 p23 - p21.2 PTPRD, PTPRD-AS2, JB175300, TYRP1, CDKN2A_p_c457_plus_2T_C, LURAP1L, MPDZ, FLJ41200, CDKN2A_p_c457_plus_1G_T, LINC00583, NFIB, TRNA_His, TRNA, CDKN2A_pR131H_c392G_A, ZDHHC21, CER1, FREM1, LOC389705, CDKN2A_p_c150_plus_2T_C, AK127963, AK021570, TTC39B, CDKN2A_pA30V_c89C_T, SNAPC3, PSIP1, CCDC171, BC042022, CDKN2A_pE26X_c76G_T, BX648501, C9orf92, BNC2, CNTLN, CDKN2A_pW15X_c44G_A, SH3GL2, MIR3152, 7SK, ADAMTSL1, CDKN2A_p_c1_minus_25C_T, DKFZp686L03130, FAM154A, RRAGA, CDKN2A_pE120K_c358G_A, SCARNA8, HAUS6, PLIN2, AK094196, CDKN2A_pW110X_c330G_A, DQ572382, DENND4C, RPS6, CDKN2A_pW110X_c329G_A, TRNA_Met, ACER2, SLC24A2, CDKN2A_pD108N_c322G_A, MIR4473, U4, MLLT3, MIR4474, CDKN2A_pE88E_c264G_A, MIR491, SNORA30, FOCAD, PTPLAD2, CDKN2A_pH83Y_c247C_T, IFNB1, IFNW1, IFNA21, IFNA4, IFNA7, CDKN2A_pR80X_c238C_T, IFNA10, IFNA16, IFNA14, IFNA17, CDKN2A_pE69X_c205G_T, IFNA22P, IFNA5, DKFZp686L0695, CDKN2A_pE61X_c181G_T, KLHL9, IFNA6, IFNA13, IFNA2, IFNA8, CDKN2A_pR58X_c172C_T, IFNA1, IFNE, MIR31HG, MIR31, MTAP, CDKN2A_p_c151_minus_1G_A, C9orf53, CDKN2A, CDKN2B, Mir_384, CDKN2A_pP48L_c143C_T, CDKN2B-AS1, CDKN2B_AS, DMRTA1, CDKN2A_pY44X_c132C_A, FLJ35282, LINC01239, CR627240, CDKN2A_pS43I_c128G_T, ELAVL2, Hel-N1, IZUMO3, JA375049, CDKN2A_pG35E_c104G_A JA374875, TUSC1, BC043546, LOC100506422
9 26,205,565 27,146,969 CN Gain 941405 p21.2 DQ598339, DQ591605, DQ574229, 0 DQ599043, DQ586829, DQ571132, DQ582785, CAAP1, PLAA, LRRC19, IFT74, TEK 9 27,146,970 27,289,413 High Copy 142444 p21.2 TEK, 5S_rRNA, LINC00032, EQTN 0 Gain Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
9 73,037,883 112,950,586 CN Gain 39912704 q21.12 - q31.3 MIR204, TRPM3, TMEM2, ABHD17B, PTCH1_pW1018X_c3054G_A, C9orf85, C9orf57, GDA, 5S_rRNA, PTCH1_pM561R_c1682T_G, AK095210, LOC100507540, ZFAND5, PTCH1_pQ417X_c1249C_T, TMC1, ALDH1A1, ANXA1, MIR6130, PTCH1_pQ365X_c1093C_T RORB, TRPM6, TRNA_Asp, C9orf40, BC043649, C9orf41, NMRK1, OSTF1, MIR548H3, PCSK5, RFK, RPSAP9, GCNT1, PRUNE2, PCA3, PCA3_1, FOXB2, VPS13A-AS1, VPS13A, GNA14, GNAQ, CEP78, PSAT1, LOC101927450, TLE4, DQ575560, DQ583878, DQ589820, DQ580124, DQ595182, DQ596925, DQ597713, DQ586158, DQ588659, DQ599976, DQ574305, DQ600106, DQ574306, DQ599155, DQ574330, DQ579956, DQ594965, DQ596802, DQ574826, DQ592136, DQ577348, DQ593172, DQ592375, DQ570523, DQ573195, DQ591664, TLE1, LOC101927502, BC036431, SPATA31D5P, DQ592725, DQ577940, DQ578305, DQ582032, DQ584769, SPATA31D4, SPATA31D3, AK097447, SPATA31D1, DQ588544, Mir_1302, RASEF, FRMD3, IDNK, UBQLN1, AK300656, GKAP1, KIF27, C9orf64, MIR7-1, HNRNPK, RMI1, LOC101927575, BX537783, SLC28A3, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
9 134,275,097 141,213,431 CN Gain 6938335 q34.13 - q34.3 PRRC2B, PRRC2B, SNORD62A, NOTCH1_pQ2460X_c7378C_T, SNORD62A, SNORD62B, LQFBS-1, NOTCH1_pL1679P_c5036T_C, POMT1, UCK1, RAPGEF1, DD413682, NOTCH1_pL1601P_c4802T_C, MED27, NTNG2, SETX, TTF1, NOTCH1_pL1594P_c4781T_C, C9orf171, BARHL1, DDX31, GTF3C4, NOTCH1_pL1586P_c4757T_C, AK8, AX748058, C9orf9, TSC1, NOTCH1_pL1575P_c4724T_C AJ011378, GFI1B, GTF3C5, MIR6877, CEL, CELP, KIAA1308, RALGDS, GBGT1, OBP2B, ABO, SURF6, MED22, SNORD24, RPL7A, SNORD36B, SNORD36A, DQ601906, SNORD36C, SURF1, SURF2, SURF4, C9orf96, REXO4, ADAMTS13, CACFD1, SLC2A6, TMEM8C, ADAMTSL2, FAM163B, DBH, DBH-AS1, SARDH, AK123314, VAV2, LINC00094, BRD3, WDR5, RNU6ATAC, RXRA, MIR4669, COL5A1, LOC101448202, MIR3689C, MIR3689D1, MIR3689A, MIR3689B, MIR3689D2, MIR3689E, MIR3689F, FCN2, FCN1, OLFM1, LOC401557, C9orf62, LOC100506599, PPP1R26- AS1, AK096249, PPP1R26, C9orf116, MRPS2, BC015688, LCN1, OBP2A, PAEP, LOC100130954, GLT6D1, LCN9, BC101937, SOHLH1, KCNT1, CAMSAP1, UBAC1, NACC2, C9orf69, 10 0 712,669 CN Loss 712670 p15.3 TUBB8,RBSG2, LHX3,ZMYND11, QSOX2, 5S_rRNA, DKFZP434A062, DIP2C, 0 DIP2C, MIR5699, PRR26 10 49,837,396 49,854,701 CN Loss 17306 q11.22 ARHGAP22 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
10 60,551,322 67,751,830 CN Gain 7200509 q21.1 - q21.3 BICC1, LINC00844, PHYHIPL, Mir_584, 0 FAM13C, SLC16A9, LINC00948, CCDC6, C10orf40, Metazoa_SRP, ANK3, CDK1, U2, RHOBTB1, LINC00845, TMEM26, BC041470, C10orf107, MIR548AV, ARID5B, RTKN2, LOC283045, ZNF365, ADO, EGR2, NRBF2, JMJD1C, AX747628, JMJD1C, MIR1296, JMJD1C-AS1, REEP3, DJ439558, ANXA2P3, DJ439576, DJ439561, CTNNA3
10 67,751,831 67,792,448 CN Loss 40618 q21.3 CTNNA3 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
10 85,557,432 105,804,295 CN Loss 20246864 q23.1 - q25.1 GHITM, BC051760, C10orf99, CDHR1, PTEN_pE7X_c19G_T, LRIT2, LRIT1, LRRC21, RGR, PTEN_pR15I_c44G_T, LINC00858, DD413707, CCSER2, PTEN_pQ17X_c49C_T, Mir_544, AK097624, GRID1-AS1, PTEN_pL23F_c69A_C, AX746544, GRID1, MIR346, WAPAL, PTEN_pP38S_c112C_T, WAPL, OPN4, LDB3, AX747977, PTEN_pL42R_c125T_G, BMPR1A, MMRN2, SNCG, AL157440, PTEN_p_c165_minus_2A_C, ADIRF, AGAP11, FAM25A, GLUD1, PTEN_pH61R_c182A_G, FAM35A, NUTM2A, NUTM2A-AS1, PTEN_pY68H_c202T_C, LOC439994, BC082979, NUTM2D, PTEN_p_c209_plus_5G_A, LINC00864, MIR4678, MINPP1, PTEN_p_c253_plus_1G_A, PAPSS2, ATAD1, CFL1P1, KLLN, PTEN, PTEN_p_c253_plus_1G_T, AK130076, RNLS, LIPJ, LIPF, LIPK, LIPN, PTEN_pH93Y_c277C_T, LIPM, ANKRD22, BC069782, PTEN_pH93Q_c279T_G, STAMBPL1, AX748062, ACTA2, FAS- PTEN_pP95L_c284C_T, AS1, FAS, HV303528, HV303525, PTEN_pI101T_c302T_C, MIR4679-2, MIR4679-1, CH25H, IFIT2, PTEN_pD107Y_c319G_T, BC040833, LIPA, IFIT3, IFIT1B, IFIT1, PTEN_pQ110X_c328C_T, IFIT5, SLC16A12, JB022994, MIR107, PTEN_pA126T_c376G_A, PANK1, FLJ37201, KRMP1, KIF20B, PTEN_pG129R_c385G_A, LINC00865, LOC101926924, PTEN_pR130X_c388C_T, AK093219, LOC101926942, PTEN_pR130Q_c389G_A, BC037970, HTR7, Y_RNA, RPP30, PTEN_pA151T_c451G_A, ANKRD1, LINC00502, NUDT9P1, PTEN_pY155C_c464A_G, PCGF5, LOC100188947, HECTD2, PTEN_pG165R_c493G_A, PPP1R3C, TNKS2-AS1, TNKS2, FGFBP3, PTEN_pQ171X_c511C_T, BTAF1, SNORA25, CPEB3, PTEN_pR173C_c517C_T, CPEB3_ribozyme, MARCH5, PTEN_pR173H_c518G_A, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
11 0 11,638,440 CN Loss 11638441 p15.5 - p15.3 LINC01001, AL137655, HRAS_pQ61H_c183G_T, LOC100133161, LOC653486, HRAS_pQ61P_c182A_C, SCGB1C1, ODF3, BET1L, MIR6743, HRAS_pQ61K_c181C_A, RIC8A, Z49985, SIRT3, PSMD13, HRAS_pG13D_c38G_A, NLRP6, ATHL1, IFITM5, IFITM2, HRAS_pG13S_c37G_A, IFITM1, IFITM3, BC040735, HRAS_pG12D_c35G_A, B4GALNT4, PKP3, SIGIRR, ANO9, HRAS_pG12S_c34G_A Metazoa_SRP, PTDSS2, RNH1, HRAS, LRRC56, C11orf35, AX748330, BC031953, RASSF7, MIR210HG, MIR210, LOC143666, PHRF1, IRF7, CDHR5, SCT, DRD4, DEAF1, TMEM80, EPS8L2, TALDO1, BC048998, PDDC1, NS3BP, CEND1, SLC25A22, PIDD, PIDD1, RPLP2, SNORA52, PNPLA2, EFCAB4A, JB050151, CD151, POLR2L, TSPAN4, AK126635, AX747537, CHID1, AP2A2, MUC6, MUC2, MUC5B, MUC5AC, MIR6744, TOLLIP, TOLLIP- AS1, BRSK2, MOB2, DUSP8, KRTAP5-1, KRTAP5-AS1, KRTAP5-2, KRTAP5-3, KRTAP5-4, KRTAP5-5, FAM99A, FAM99B, AF085962, KRTAP5-6, IFITM10, CTSD, SYT8, TNNI2, MIR4298, LSP1, TNNT3, MRPL23, AK126380, MRPL23-AS1, AK311497, H19, MIR675, MIR483, IGF2, IGF2-AS, 11 11,638,440 13,150,261 CN Gain 1511822 p15.3 - p15.2 GALNT18,INS-IGF2, INS, MIR4299, TH, MIR4686, MIR8070, ASCL2, USP47, 0 DKK3, MIR6124, MICAL2, AK026905, MICALCL, PARVA, DD413619, TEAD1, SCARNA16, LINC00958, LOC100506305, RASSF10 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
11 13,150,261 13,436,450 High Copy 286190 p15.2 ARNTL, 7SK, BTBD10 0 Gain 11 13,436,450 22,045,341 CN Gain 8608892 p15.2 - p14.3 BTBD10, PTH, FAR1, SPON1, RRAS2, 0 COPB1, U7, PSMA1, PDE3B, CYP2R1, CALCA, CALCB, INSC, SnoMBII_202, MIR6073, SOX6, Metazoa_SRP, C11orf58, AL833346, PLEKHA7, OR7E14P, SNORD14, RPS13, PIK3C2A, NUCB2, AK096475, NCR3LG1, KCNJ11, ABCC8, USH1C, OTOG, MYOD1, KCNC1, SERGEF, TPH1, SAAL1, SAA3P, MRGPRX3, MRGPRX4, LOC494141, SAA4, SAA2-SAA4, SAA2, SAA1, HPS5, GTF2H1, LDHA, LDHC, LDHAL6A, TSG101, JA429845, UEVLD, SPTY2D1- AS1, SPTY2D1, TMEM86A, IGSF22, PTPN5, MRGPRX1, MRGPRX2, ZDHHC13, Mir_340, CSRP3, E2F8, NAV2-AS5, NAV2-AS4, MIR4486, SNORA1, LOC100126784, NAV2, MIR4694, DBX1, TRNA, HTATIP2, PRMT3, SLC6A5, NELL1
11 26,084,277 26,110,050 CN Loss 25774 p14.3 - p14.2 0 0 11 27,682,693 28,114,125 CN Gain 431433 p14.1 BDNF-AS, BDNF, MIR610, JB074938, 0 KIF18A 11 28,114,126 28,452,521 High Copy 338396 p14.1 KIF18A, METTL15 0 Gain 11 28,452,522 28,566,789 CN Gain 114268 p14.1 MIR8068 0 11 28,566,790 29,034,634 High Copy 467845 p14.1 0 0 Gain Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
11 29,062,789 29,110,258 High Copy 47470 p14.1 0 0 Gain 11 29,272,732 34,694,617 CN Gain 5421886 p14.1 - p13 KCNA4, FSHB, ARL14EP, Mir_633, WT1_pR394W_c1180C_T, MPPED2, DCDC5, DCDC1, DNAJC24, WT1_pR390X_c1168C_T, IMMP1L, ELP4, PAX6, PAUPAR, WT1_pG379V_c1136G_T, DKFZp686K1684, RCN1, U3, WT1, WT1_pR362X_c1084C_T, WT1-AS, WT1, EIF3M, CCDC73, WT1_pS313X_c938C_A, PRRG4, QSER1, DEPDC7, TCP11L1, WT1_pR301X_c901C_T, LINC00294, CSTF3, CSTF3-AS1, HIPK3, WT1_pF154S_c461T_C, KIAA1549L, C11orf91, CD59, FBXO3, WT1_pS46X_c137C_A LMO2, CAPRIN1, NAT10, ABTB2, CAT, ELF5, EHF 11 34,752,447 37,597,733 CN Gain 2845287 p13 - p12 APIP, MIR1343, PDHX, CD44, SLC1A2, 0 PAMR1, FJX1, TRIM44, DQ573949, Mir_652, MIR3973, BC036209, LDLRAD3, COMMD9, PRR5L, TRAF6, RAG1, RAG2, C11orf74 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
11 71,188,902 73,965,549 CN Loss 2776648 q13.4 NADSYN1, KRTAP5-7, KRTAP5-8, 0 KRTAP5-9, KRTAP5-10, KRTAP5-11, FAM86C1, ALG1L9P, ZNF705E, DEFB108B, LOC100129216, LOC100133315, RNF121, IL18BP, LOC100128494, NUMA1, MIR3165, LRTOMT, LAMTOR1, ANAPC15, FOLR3, FOLR1, FOLR2, INPPL1, PHOX2A, CLPB, AL832797, MIR139, PDE2A, BC150585, ARAP1, STARD10, MIR4692, ATG16L2, FCHSD2, P2RY2, P2RY6, ARHGEF17, RELT, FAM168A, PLEKHB1, RAB6A, MRPL48, COA4, PAAF1, DNAJB13, UCP2, UCP3, C2CD3, PPME1, SNORA7, P4HA3
12 169,821 1,143,708 CN Gain 973888 p13.33 IQSEC3, LOC574538, SLC6A12, 0 LOC101929384, SLC6A13, LOC102723544, KDM5A, CCDC77, B4GALNT3, NINJ2, LOC100049716, U4atac, WNK1, HSN2, AK128619, RAD52, BC039168, ERC1 12 1,231,447 1,654,094 CN Gain 422648 p13.33 ERC1, LINC00942, AX746535 0 12 2,160,748 3,577,145 CN Gain 1416398 p13.33 - p13.32 AK308652, CACNA1C-AS4, CACNA1C- 0 IT3, CACNA1C, Mir_584, CACNA1C- AS2, CACNA1C-AS1, LOC283440, FKBP4, ITFG2, NRIP2, LOC100507424, FOXM1, RHNO1, TULP3, TEAD4, TSPAN9, AK056228, AK095365, BC047090, DQ574680, DQ597527, DQ591569, DQ590472, PRMT8 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
12 5,314,214 6,032,797 CN Loss 718584 p13.32 - p13.31 LOC101929584, BC031884, NTF3, 0 ANO2 12 6,426,433 7,806,728 CN Loss 1380296 p13.31 PLEKHG6, TNFRSF1A, SCNN1A, LTBR, 0 CD27-AS1, CD27, TAPBPL, VAMP1, MRPL51, SCARNA10, NCAPD2, GAPDH, DL491527, IFFO1, NOP2, SCARNA11, AK096395, CHD4, LPAR5, ACRBP, ING4, ZNF384, PIANP, COPS7A, MLF2, PTMS, LAG3, CD4, GPR162, LEPREL2, GNB3, AK097957, CDCA3, USP5, TPI1, SPSB2, RRPL13L, RPL13P5, DSTNP2, LRRC23, ENO2, ATN1, C12orf57, PTPN6, MIR200C, MIR141, SCARNA12, PHB2, EMG1, LPCAT3, C1S, C1R, C1RL, C1RL-AS1, RBP5, CLSTN3, PEX5, ACSM4, CD163L1, CD163, APOBEC1
12 7,806,728 8,485,813 CN Gain 679086 p13.31 APOBEC1, GDF3, DPPA3, CLEC4C, 0 NANOGNB, NANOG, Y_RNA, SLC2A14, NANOGP1, AY455283, SLC2A3, FOXJ2, C3AR1, BC039122, NECAP1, CLEC4A, POU5F1P3, ZNF705A, FAM66C, FAM90A1, FAM86FP, LOC101927905 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
12 8,485,813 32,425,114 CN Loss 23939302 p13.31 - p11.21 LINC00937, CLEC6A, CLEC4D, CLEC4E, KRAS_pA146T_c436G_A, AICDA, MFAP5, RIMKLB, A2ML1, KRAS_pQ61H_c183A_C, PHC1, M6PR, KLRG1, LINC00612, A2M-KRAS_pQ61P_c182A_C, AS1, A2M, JB175316, PZP, A2MP1, KRAS_pQ61K_c181C_A, MIR1244-1, MIR1244-2, MIR1244-3, KRAS_pA59T_c175G_A, LINC00987, LOC100499405, KRAS_pG13D_c38G_A, SNORA75, LOC642846, DQ582774, KRAS_pG13S_c37G_A, DQ586985, DQ577612, DQ586485, KRAS_pG12D_c35G_A, DQ577180, DQ585706, DQ575612, KRAS_pG12S_c34G_A DQ592342, LOC101928030, LOC101930452, DQ599803, DDX12P, SNORA75, BX647938, KLRB1, LOC374443, CLEC2D, CLECL1, CD69, KLRF1, CLEC2B, KLRF2, CLEC2A, LOC100506159, CLEC12A, CLEC1B, CLEC12B, LOC102724020, CLEC9A, CLEC1A, CLEC7A, OLR1, BC055085, TMEM52B, GABARAPL1, KLRD1, LOC101928100, AK096314, KLRK1, KLRC4-KLRK1, KLRC4, KLRC3, KLRC2, KLRC1, KLRAP1, MAGOHB, STYK1, YBX3, LOC101928162, TAS2R7, TAS2R8, TAS2R9, TAS2R10, PRR4, TAS2R13, PRH2, TAS2R14, TAS2R50, TAS2R20, PRH1-PRR4, TAS2R19, PRH1, TAS2R31, TAS2R46, TAS2R43, PRB4, TAS2R30, LOC100129361, 12 32,996,159 34,244,646 CN Loss 1248488 p11.21 - p11.1 PKP2,TAS2R42, SYT10, PRB3, ALG10 PRB1, PRB2, 0 12 72,458,905 75,122,435 CN Loss 2663531 q21.1 TRHDE-AS1, BC093903, TRHDE, 0 LOC101928137, LOC100507377, TRNA_Gln, ATXN7L3B Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
13 19,020,013 32,178,877 CN Loss 13158865 q11 - q12.3 LINC00417, DQ586768, DQ579288, FLT3_pD835E_c2505T_G, DQ587539, ANKRD20A9P, BC035261, FLT3_pD835V_c2504A_T_allele1, LINC00408, DQ572285, LINC00442, FLT3_pD835N_c2503G_A, RNU6-52P, TUBA3C, ANKRD26P3, FLT3_pL561L_c1683A_G LINC00421, TPTE2, MPHOSPH8, PSPC1, ZMYM5, BC044596, ZMYM2, GJA3, GJB2, GJB6, MIR4499, CRYL1, IFT88, IL17D, AK055408, N6AMT2, XPO4, LINC00367, LATS2, SAP18, SKA3, MRPL57, MRP63, LINC00539, MIPEPP3, ZDHHC20, MICU2, FGF9, Metazoa_SRP, LINC00424, AK054845, BC035104, LINC00540, BC048997, BASP1P1, SGCG, SACS, SACS-AS1, LINC00327, TNFRSF19, MIPEP, C1QTNF9B-AS1, C1QTNF9B, ANKRD20A19P, BC043582, SPATA13, MIR2276, SPATA13-AS1, C1QTNF9, BC038727, PARP4, TPTE2P6, ATP12A, RNF17, CENPJ, AK054988, TPTE2P1, PABPC3, AMER2, LOC101928922, BC022569, LOC102723318, MTMR6, NUPL1, ATP8A2, SHISA2, RNF6, CDK8, BC047364, WASF3, GPR12, USP12, USP12-AS1, USP12-AS2, LINC00412, RPL21P28, RPL21, SNORD102, SNORA27, RASL11A, GTF3A, MTIF3, LNX2, POLR1D, GSX1, PDX1-AS1, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
13 32,178,877 33,860,144 Homozygou 1681268 q12.3 - q13.1 RXFP2, EEF1DP3, DKFZp666K117, BRCA2_pR18H_c53G_A, s Copy Loss BC035084, FRY-AS1, FRY, ZAR1L, BRCA2_pE187K_c559G_A, BRCA2, N4BP2L1, SNORA16, BRCA2_pT630I_c1889C_T, HV983084, N4BP2L2, MINOS1P1, BRCA2_pP920S_c2758C_T, N4BP2L2-IT2, U50535, BC026240, BRCA2_pI1017S_c3050T_G, PDS5B, LINC00423, KL, STARD13-AS, BRCA2_pG1338G_c4014C_T, STARD13 BRCA2_pE1593X_c4777G_T, BRCA2_pS1682S_c5046T_C, BRCA2_pV1988I_c5962G_A, BRCA2_pH2415N_c7243C_A, BRCA2_pR2678S_c8034G_T, BRCA2_pR2787H_c8360G_A, BRCA2_pR2842C_c8524C_T, BRCA2_pQ2934X_c8800C_T, BRCA2_pD3095E_c9285C_A, BRCA2_pI3103M_c9309A_G, BRCA2_pR3128X_c9382C_T Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
13 33,860,144 109,025,409 CN Loss - 75165266 q13.1 - q33.3 STARD13, U5, RFC3, LINC00457, RB1_pE54X_c160G_T, includes NBEA, MAB21L1, MIR548F5, DCLK1, RB1_pS82X_c245C_A, RB1 TRNA_Pseudo, SOHLH2, CCDC169- RB1_p_c380_plus_1G_A, SOHLH2, CCDC169, U6, SPG20, RB1_pE137X_c409G_T, SPG20OS, CCNA1, SERTM1, 5S_rRNA, RB1_pQ217X_c649C_T, RFXAP, SMAD9, ALG5, EXOSC8, RB1_pR251X_c751C_T, SUPT20H, CSNK1A1L, LINC00547, RB1_pR320X_c958C_T, POSTN, TRPC4, Mir_720, LINC00571, RB1_pR358X_c1072C_T, UFM1, LINC00366, FREM2, STOML3, RB1_pQ395X_c1183C_T, PROSER1, NHLRC3, LHFP, AK021977, RB1_p_c1215_plus_1G_A, MIR4305, COG6, LINC00332, RB1_pE440X_c1318G_T, LINC00548, 7SK, LINC00598, FOXO1, RB1_pR445X_c1333C_T, MIR320D1, MRPS31, SLC25A15, RB1_pR455X_c1363C_T, MIR621, TPTE2P5, SUGT1P3, ELF1, RB1_p_c1499_minus_1G_T, TRNA_Glu, WBP4, KBTBD6, RB1_pR552X_c1654C_T, LOC101929140, AK056182, KBTBD7, RB1_pR556X_c1666C_T, BC051736, MTRF1, Mir_324, NAA16, RB1_pR579X_c1735C_T, U6, OR7E37P, RGCC, MIR5006, VWA8, RB1_p_c1961_minus_1G_A, Mir_684, VWA8-AS1, DGKH, RB1_pQ685X_c2053C_T, AK054970, AKAP11, TNFSF11, RB1_pQ702X_c2104C_T, FAM216B, EPSTI1, DNAJC15, RB1_p_c2107_minus_2A_G, LINC00400, ENOX1-AS2, ENOX1, RB1_pE748X_c2242G_T, CCDC122, LACC1, LINC00284, SMIM2- RB1_p_c2326_minus_2A_C, AS1, SMIM2, MGC5590, SMIM2-IT1, RB1_pR787X_c2359C_T MIR8079, AX748251, SERP2, BC025370, TUSC8, TSC22D1, TSC22D1- AS1, LINC00330, TRNA, NUFIP1, GPALPP1, KIAA1704, LOC101929259, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
13 111,794,504 113,487,192 CN Loss 1692689 q34 ARHGEF7-AS1, LOC101060553, 0 ARHGEF7, AX748212, TEX29, LINC00354, LINC00403, SOX1, AK055145, LINC01070, CR627049, LOC101928730, SPACA7, TUBGCP3, C13orf35, ATP11AUN, BC041346, ATP11A-AS1, AX748036, ATP11A
16 34,196,182 34,920,840 CN Loss 724659 p11.2 - p11.1 UBE2MP1, LOC283914, LOC146481, 0 LOC100130700 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
16 46,455,960 90,354,753 CN Loss 43898794 q11.2 - q24.3 ANKRD26P1, SHCBP1, VPS35, ORC6, CDH1_p_c1009_minus_1G_A, MYLK3, C16orf87, GPT2, DNAJA2, CDH1_pI374I_c1122C_T NETO2, LOC101927102, ITFG1, Y_RNA, PHKB, BC048130, LOC100507534, LOC101927132, ABCC12, ABCC11, LONP2, MIR548AE2, LOC100507577, SIAH1, N4BP1, U6, CBLN1, C16orf78, ZNF423, CNEP1R1, HEATR3, AF086132, PAPD5, ADCY7, MIR6771, BRD7, SNORD112, NKD1, LOC101927272, AF143871, SNX20, NOD2, CYLD, LOC101927334, SALL1, LOC101927364, C16orf97, LINC00919, LOC102467079, TOX3, LINC00918, CASC16, CHD9, LOC643802, LOC102723373, RBL2, AKTIP, RPGRIP1L, FTO, JB149426, FTO- IT1, IRX3, CRNDE, IRX5, IRX6, MMP2, LPCAT2, CAPNS2, SLC6A2, CES1P2, CES1P1, CES1, CES5A, LOC283856, DKFZP434H168, MIR3935, GNAO1, AMFR, NUDT21, OGFOD1, BBS2, MT4, MT3, MT2A, MT1L, MT1A, MT1M, MT1E, MT1JP, MT1DP, MT1B, MT1F, MT1G, MT1H, MTE, MT1IP, MT1X, NUP93, MIR138-2, SLC12A3, MIR6863, HERPUD1, CETP, NLRC5, CPNE2, FAM192A, RSPRY1, ARL2BP, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
17 7,506,837 7,671,804 CN Loss 164968 p13.1 FXR2, TRNA_Pseudo, SHBG, SAT2, TP53_pR342X_c1024C_T, includes ATP1B2, HV941431, HV941433, TP53_pE336X_c1006G_T, TP53 HV941428, HV941434, HV941486, TP53_pQ331X_c991C_T, HV941429, TP53, HV941440, TP53_p_c920_minus_1G_A, HV941478, HV941442, HV941444, TP53_pR306X_c916C_T, HV941430, WRAP53, EFNB3, TP53_pE298X_c892G_T, RPL29P2, DNAH2 TP53_pE285K_c853G_A, TP53_pR273H_c818G_A, TP53_pR273C_c817C_T, TP53_pG266E_c797G_A, TP53_p_c782_plus_1G_T, TP53_pR249S_c747G_T, TP53_pR248Q_c743G_A, TP53_pR248W_c742C_T, TP53_pG245S_c733G_A, TP53_pY236C_c707A_G, TP53_p_c672_plus_1G_A, TP53_pY220C_c659A_G, TP53_pR213X_c637C_T, TP53_pR196X_c586C_T, TP53_pH193R_c578A_G, TP53_pH179Q_c537T_G, TP53_pH179R_c536A_G, TP53_pC176F_c527G_T, TP53_pR175H_c524G_A, TP53_pY163C_c488A_G, TP53_pA159V_c476C_T, 17 7,728,166 7,760,539 CN Loss 32374 p13.1 DNAH2, KDM6B, TMEM88, LSMD1, TP53_pR158H_c473G_A, 0 NAA38 17 60,940,628 61,006,083 CN Loss 65456 q23.2 MIR548W 0 17 61,144,186 61,439,735 CN Loss 295550 q23.3 MIR548W, TANC2 0 17 61,454,707 61,650,448 CN Loss 195742 q23.3 TANC2, CYB561, ACE, KCNH6, DCAF7 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
18 41,334,022 41,339,844 CN Gain 5823 q12.3 0 0 19 6,531,407 6,609,287 CN Loss 77881 p13.3 TNFSF9, CD70 0 20 0 14,782,559 CN Loss 14782560 p13 - p12.1 DEFB125, DEFB126, DEFB127, PAK7_pT397K_c1190C_A DEFB128, DEFB129, DEFB132, C20orf96, ZCCHC3, LOC100507459, SOX12, NRSN2, TRIB3, RBCK1, DQ588114, TBC1D20, CSNK2A1, TCF15, SRXN1, SCRT2, SLC52A3, FAM110A, ANGPT4, RSPO4, PSMF1, TMEM74B, C20orf202, RAD21L1, SNPH, SDCBP2, FKBP1A-SDCBP2, SDCBP2-AS1, FKBP1A, MIR6869, NSFL1C, SIRPB2, SIRPD, SIRPB1, AK093519, LOC101929010, SIRPG, LOC100289473, SIRPA, AK090681, PDYN, STK35, LOC388780, TGM3, TGM6, SNORD119, SNRPB, AK126717, ZNF343, TMC2, MIR1292, SNORD110, SNORA51, NOP56, SNORD86, SNORD56, SNORD57, IDH3B, EBF4, CPXM1, C20orf141, TMEM239, PCED1A, VPS16, PTPRA, GNRH2, MRPS26, OXT, AVP, UBOX5-AS1, UBOX5, FASTKD5, LZTS3, DDRGK1, ITPA, SLC4A11, C20orf194, U6, ATRN, GFRA4, AX748440, ADAM33, SIGLEC1, HSPA12B, C20orf27, SPEF1, CENPB, CDC25B, LOC101929125, BC042140, AP5S1, MAVS, BC012193, PANK2, 20 14,782,560 14,827,300 Homozygous Copy 44741Loss p12.1 MACROD2,MIR103A2, MIR103B2,MACROD2 RNF24, 0 Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
20 14,827,301 26,319,438 CN Loss 11492138 p12.1 - p11.1 MACROD2, MACROD2-AS1, 0 MACROD2, AK125594, Mir_584, KIF16B, SNRPB2, OTOR, PCSK2, BFSP1, DSTN, RRBP1, BANF2, TRNA_Gln, SNX5, SNORD17, AK296947, MGME1, JB175279, OVOL2, PET117, CSRP2BP, ZNF133, BC043266, LINC00851, DZANK1, MIR3192, POLR3F, RBBP9, SEC23B, LINC00493, DTD1, LOC101929526, LINC00652, LOC100270804, SCP2D1, C20orf78, LOC100130264, SLC24A3, Mir_548, BC090059, DQ594620, DQ573663, RIN2, NAA20, CRNKL1, C20orf26, INSM1, RALGAPA2, BC042893, PLK1S1, KIZ, LOC101929591, BC034426, XRN2, NKX2-4, NKX2-2, LOC101929625, Nkx2_2as, LOC101929608, PAX1, LOC100270679, CR627206, LOC101929663, LOC284788, LINC00261, FOXA2, LOC101929685, AK055550, BC045663, SSTR4, AX747264, THBD, CD93, LINC00656, AX747171, NXT1, LOC100505683, GZF1, NAPB, CSTL1, CST11, CST8, CST13P, CST9L, CST9, CST3, CST4, X 23,428,703 23,458,054 CN Loss 29352 p22.11 CST1, CST2, CST5, GGTLC1, 0 0 X 150,801,467 151,067,028 CN Loss 265562 q28 PASD1, PRRG3, FATE1, CNGA2 0 Y 1 59,373,566 CN Loss - 59373566 p11.32 - q12 PLCXD1, GTPBP6, LINC00685, 0 includes PPP2R3B, SHOX, DQ576039, CSF2RA, PCDH11Y MIR3690, IL3RA, CRLF2, SLC25A6, Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press
Whole Genome Sequencing identifies homozygous BRCA2 deletion guiding treatment in de-differentiated prostate cancer
Karin Purshouse, Anna Schuh, Benjamin P Fairfax, et al.
Cold Spring Harb Mol Case Stud published online March 9, 2017 Access the most recent version at doi:10.1101/mcs.a001362
Supplementary http://molecularcasestudies.cshlp.org/content/suppl/2017/03/09/mcs.a00136 Material 2.DC1
Published online March 9, 2017 in advance of the full issue.
Accepted Peer-reviewed and accepted for publication but not copyedited or typeset; Manuscript accepted manuscript is likely to differ from the final, published version. Published onlineMarch 9, 2017in advance of the full issue.
Creative This article is distributed under the terms of the Commons http://creativecommons.org/licenses/by/4.0/, which permits unrestricted reuse and License redistribution provided that the original author and source are credited.
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