C-55 (Comprehensive Panel) Pathogenic Variant Detected

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Capﬆone Healthcare 8601 Dunwoody Place, Building 400, Suite 444 Atlanta, GA 30350 www.capﬆonehealthcare.com 844-497-8851 Laboratory Director: John Hanson, PhD CLIA ID Number: 11D2073885

PATIENT INFORMATION PROVIDER INFORMATION SPECIMEN Patient Name: Sarah Doe Physician: Dr Jospeh Smith Accession ID: 10000520 Date of Birth: Apr 10, 1985 Client: St Michael Hospital Specimen Type: Buccal Swab Age: 33 Client ID: 123654 Collection Date: Aug 21, 2018 Sex: Female Date Accessioned: Aug 22, 2018 Ethnicity: Caucasian Date Reported: Sep 7, 2018

TEST PERFORMED

C-55 (Comprehensive Panel) Targeted next-generation sequencing was performed on this specimen. See Methods and Limitations section for more information.

RESULT

Pathogenic Variant Detected

An abnormality is detected that has been reported to be associated with an increased risk for hereditary cancer. This ﬁnding may help you and your doctor make more informed choices about your health care and develop a ﬆrategy for cancer prevention and monitoring.

VARIANT SUMMARY Variants Detected Genotype Phenotype Assessment BRCA1 Susceptibility To Familial c.798_799delTT Heterozygous Breaﬆ-ovarian Cancer Pathogenic p.S267fs*19 Type 1

VARIANT INTERPRETATION BRCA1 Interpretation: BRCA1 is a tumor suppressor responsible for repair of DNA double ﬆrand c.798_799delTT breaks and maintenance of genomic ﬆability [3]. Deletions, loss of heterozygosity, and loss-of- function mutations cause BRCA1 inactivation [7, 6]. p.S267fs*19 Pathogenic

GENES TESTED APC, ATM, AXIN1, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDC73, CDH1, CDKN1C, CDKN2A, CHEK2, DICER1, DIS3L2, EPCAM, FH, FLCN, GPC3, GREM1, MEN1, MET, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PAKAR1A, PALB2, PMS2, POLD1, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RB1, REQL4, RET, SDHA, SDHB, SDHC, SDHD, SMAD4, SMARC4A, STK11, SUFU, TP53, TSC1, TSC2, VHL, WT1

METHODS AND LIMITATIONS DNA extracted from patient’s saliva sample is quantified using Qubit 2.0 Fluorimeter (Life Technologies Inc.). Germline mutations of APC, ATM, AXIN1, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDC73, CDH1, CDKN1C, CDKN2A, CHEK2, DICER1, DIS3L2, EPCAM, FH, FLCN, GPC3, GREM1, MEN1, MET, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PAKAR1A, PALB2, PMS2, POLD1, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RB1, REQL4, RET, SDHA, SDHB, SDHC, SDHD, SMAD4, SMARC4A, STK11, SUFU, TP53, TSC1, TSC2, VHL, WT1 genes are teﬆed by sequencing the entire coding region for each gene with 5 bp of padding at both ends. The panel consiﬆs of amplicons that cover 98% of all coding regions of the genes liﬆed above. Each sample template is tagged with a unique barcode for sample identification before processing. Sequencing is performed on the Ion Torrent S5 (Life Technologies Inc.) using AmpliSeq and Ion Chef technologies, and Hi-Q View chemiﬆry. Data obtained are analyzed using the Applied Biosyﬆems Ion Torrent variant analyzing software, which includes signal processing, base calling,quality score assignment, adapter trimming, alignment to human genome 19 reference (hg19), coverage analysis, and variant calling. Variant annotation is performed on the QIAGEN Clinical Insight software. Sanger sequencing confirmation is performed on all pathogenic, likely pathogenic, and variant of unknown significance samples through Eurofins Clinical Molecular Teﬆing Services, LLC.

Based on validation ﬆudies, our method has a >95% sensitivity and speciﬁcity for detecting single nucleotide variants, insertions/deletions, and other frame shift mutations. However, some rare and novel genetic variations might not be detected by this method. Genes other then those liﬆed above that are associated with certain types of cancer are beyond the scope of this teﬆ.

QIAGEN Clinical Insight (QCITM) is a variant analysis, interpretation and decision support tool for research and clinical labs analyzing human genetics data and is not intended to be used for diagnoﬆic purposes. QCI Interpret software includes the following underlying databases, data reference sets and tools; QIAGEN Clinical Insight-Interpret (5.3.20180727), Ingenuity Knowledge Base (Rohan 180831.001), CADD (v1.3), Allele Frequency Community (2018-05-25), EVS (ESP6500SI-V2), JASPAR (2013-11), Ingenuity Knowledge Base Snapshot Timeﬆamp (2018-08-31 11:07:19.0), Viﬆa Enhancer hg18 (2012- 07), Viﬆa Enhancer hg19 (2012-07), Clinical Trials (Rohan 180831.001), PolyPhen-2 (v2.2.2), 1000 Genome Frequency (phase3v5b), ExAC (0.3.1), iva (Jun 26 11:55 iva-1.0.476233.jar), PhyloP hg18 (2009-11), PhyloP hg19 (2009-11), DbSNP (151), TargetScan (6.2), CentoMD (4.2), OMIM (May 26, 2017), gnomAD (2.0.1), BSIFT (2016-02-23), TCGA (2013-09-05), Clinvar (2018-04-06), DGV (2016-05-15), COSMIC (v84), HGMD (2018.1), SIFT4G (2016-02-23)

DISCLAIMER False positives and false negatives are possible. Such errors can be due to contamination, technical errors, and interference from rare genetic variants. It is recommended to consider alternative methods before taking any clinical action. Consulting your results with a genetic counselor is highly recommended. This teﬆ was developed, and its performance characteriﬆics determined by Capﬆone Healthcare. The laboratory is regulated and accredited by CLIA and the Joint Commission (JCHO) as qualiﬁed to perform high-complexity teﬆing. This teﬆ is used for clinical purposes. It should not be regarded as inveﬆigational or for research.

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2. Crawford B, Adams SB, Sittler T, van den Akker J, Chan S, Leitner O, Ryan L, Gil E, van 't Veer L (2017) Multi-gene panel teﬆing for hereditary cancer predisposition in unsolved high-risk breaﬆ and ovarian cancer patients. Breaﬆ Cancer Res Treat. 2017 Jun;163(2):383-390. Epub 2017 Mar 9 (PMID: 28281021)

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