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12/28/2018 Supplement R2.htm Supplemental Table 1. Exome variant filtering strategy Steps Strategy taken Start Total variants called across family members with Step 1 Excluding synonymous variants Step 2 Excluding segmental duplicaons >2 a Step 3 Excluding variants with MAF >3% in ExAC, 1000Genomes or ESP Step 4 Excluding variants that appear >2 mes in an internal control populaon Step 5 Excluding variants that do not appear in the DBA cases and obligate carriers a Based on UCSC genomicSuperDups track Abbreviations: MAF: minor allele frequency; ESP: Exome sequencing project variant database Supplemental Table 2. Primer sequences used in variant validation by family and gene Gene Chromosome Posion Reference Variant Panel/Primers Forward primer Reference primer nucleode nucleode CAGCTTGTATTCCTCTTCTTTCCCT RPL35A chr3 197680960 T A Ion AmpliSeq Designer GATTCATCAGACGTCCATTTTGCTAAA RPL15 chr3 23960685 A G Ion Torrent PGM Sequencer/IDT Primers AAAGACTCTTGTCTGGTGGTGAAC GACTCTCAGAGCCCCACAGTG RPL5 chr1 93306307 T C Ion Torrent PGM Sequencer/IDT Primers GACTGTTGGTGTAATTGTGC TCTGAGGCTAACACATTTCCATC RPL35 chr9 127620338 C G Ion Torrent PGM Sequencer/IDT Primers ATCAGTGGAAGTGCCAGGAAAC GGTCCTTGGATTCACCCTGC RPL18 chr19 49120619 A G Ion AmpliSeq Designer CCTCCCTTCCAGACAGACAAG TCATCATGTGTTTGCCCCTTCA RPS19 chr19 42365221 A C Ion AmpliSeq Designer GGCACAGCATAGTTGTGTTGAG CAGAGGAGACAGGGAAGTATGGT RPL4 chr15 66791818 G C Ion AmpliSeq Designer AAAAATTCTAACCAAGCTTTACA GTGTTAAGAAGCAGAAGAAGCCTCT GAGCA RPS10 chr6 34392470 C A Ion AmpliSeq Designer TTGTCCCTTACACAAAAGAAACTATCTTCA GCTTCTACTTAACGCCTTAACAGTAGT RPS19 chr19 42365276 G T Ion AmpliSeq Designer GGCACAGCATAGTTGTGTTGAG CAGAGGAGACAGGGAAGTATGGT RPS19 chr19 42375419 G T Ion AmpliSeq Designer GGGAATACCCACAGTGAGAATTAGAT AAAAAGAGACCCAGACCAGGATTAC RPS26 chr12 56435951 A G Ion AmpliSeq Designer GTTCTTGAAGCCCGTCTCCTA CAAATGAAATGTACACTCGGTCCAC Supplemental Table 3. Genes of interest in DBA included in array Comparative Genomic Hybridization (aCGH) Genes of interest in Diamond-Blackfan Anemia BMS1 RPL21 RPL3L RPS23 EMG1 RPL22 RPL4 RPS24 FAU RPL22L1 RPL41 RPS25 FCF1 RPL23 RPL5 RPS26 IMP3 RPL23A RPL6 RPS27 IMP4 RPL24 RPL7 RPS27A LSG1 RPL26 RPL7A RPS27L NHP2L1 RPL26L1 RPL7L1 RPS28 NMD3 RPL27 RPL8 RPS29 NOB1 RPL27A RPL9 RPS3 RCL1 RPL28 RPLP0 RPS3A REXO1 RPL29 RPLP1 RPS4X REXO2 RPL3 RPLP2 RPS4Y1 RMRP RPL30 RPS10 RPS4Y2 RPL10 RPL31 RPS11 RPS5 RPL10A RPL32 RPS12 RPS6 RPL10L RPL34 RPS13 RPS7 RPL11 RPL35 RPS14 RPS8 RPL12 RPL35A RPS15 RPS9 RPL13 RPL36 RPS15A RPSA RPL13A RPL36A RPS16 RRP7 RPL14 RPL36AL RPS17L UBA52 RPL15 RPL37 RPS18 UTP14A RPL17 RPL37A RPS19 UTP14C RPL18 RPL38 RPS2 XRN1 RPL18A RPL39 RPS20 XRN2 RPL19 RPL39L RPS21 file:///X:/jmedgenet/Issue%20makeup/jmedgenet_54_6/Supplement%20R2.htm 1/6 12/28/2018 Supplement R2.htm Supplemental Table 4A. Summary of novel mutations in known DBA ribosomal genes discovered by Whole Exome Sequencing mily ID, NCI-249, NCI-301, NCI-319, NCI-359, NCI-391, NCI-2, RPL35A NCI-56, RPL15 NCI-81, RPL5 RPS19 RPS10 RPS19 RPS19 RPS26 d 3q29 3p24.2 1p22.1 19q13.2 6p21.31 19q13.2 19q13.2 12q13.2 c a g.197680960T>A g.23960685A>G g.93306307T>C g.42365221A>C g.34392470G>T g.42365276G>T g.42375419G>T g.56435951A>G acid p.V84D p.V103A p.K38Q p.E100X p.R56L p.V138L p.M1V c.310-2A>G hangeb GTT>GaT predicted splice CTG>CcG AAG>cAG GAG>tAG CGA>CtA GTG>tTG ATG>gTG site llele Not reported Not reported Not reported Not reported Not reported Not reported Not reported Not reported cyc Probably Probably Probably Probably Possibly en-2 N/A N/A Benign damaging damaging damaging damaging damaging Deleterious N/A Deleterious Deleterious N/A Deleterious Tolerated Deleterious Disease-causing n Taster Disease-causing Disease-causing Disease-causing Disease-causing Disease-causing Disease-causing Disease-causing (automatic) M Deleterious N/A Tolerated Deleterious N/A Deleterious Deleterious Deleterious core 15.38 16.19 N/A 12.5 18.78 10.76 13.46 14.31 + score 5.35 5.83 5.68 4.57 5.19 4.57 4.52 5.92 on based on the reference human genome UCSC build hg19/Genome Reference Consortium GRCh37 ase letter indicates the mutant nucleotide ed in 1000Genomes, ESP and ExAC Supplemental Table 4B. Summary of deletions in known DBA ribosomal genes discovered by deletion analyses CI Family ID, NCI-418, NCI-51, RPS17del NCI-71, RPL35Adel NCI-76, RPS26del NCI-312, RPS17del ene RPL35Adel ne cytoband 15q25.2 3q29 12q13.2 15q25.2 3q29 undaries of chr15: 5:82,993,199- chr3:195,507,436- chr12: ~56,425,760- chr15: ~83,195,579- chr3: ~197,674,279- letiona 84,790,612 198,022,430 56,447,522 84,832,932 197,692,417 ze of deletion 1,797,413 bp* 2,514,994 bp* At least 23,698 bp* At least 1,614,662 bp* At least 18,138 bp* ne start position 83,205,501 197,677,052 56,435,686 83,205,501 197,677,052 ne end position 83,209,295 197,682,721 56,438,007 83,209,295 197,682,721 on based on the reference human genome UCSC build hg19/Genome Reference Consortium GRCh37 of the entire coding sequence Supplemental Table 5. Clinical characteristics of affected participants with causative genetic changes in known ribosomal genes eADA Epo Initial Hb MCV elation Age† Dysmorphology and Other (IU/g HbF Gender Gene hematopoietic Treatment†† (gm/dL) (fL) (mU/ (years) Clinical Features Hb) (%)††† Ship symptoms ††† ††† ml) ††† ††† hypospadias, absent left kidney, steroid responsive until age 13, roband male 14.05 RPL35A anemia at birth 5.6 106 0.91 6.8 580.1 presacral dimple, snub nose then transfusion dependent short stature, shield chest, short anemia at age steroid responsive with roband female 28.21 RPS17 web neck, scoliosis, spine 10 105 0.77 6.3 1291 6 months intermittent transfusions compression fracture developmental delay, cerebral steroids and transfusions, in roband male 3.11 RPL15 anemia at birth palsy, radioulnar synostosis, 7.2 91 2.41 14.9 N/A remission horseshoe kidney anemia at age developmental delay, short steroid responsive, with roband female 24.75 RPL35A 10.9 95 0.91 4.1 124.5 1 year stature, failure to thrive neutropenia no dysmorphology reported. steroid responsive, stopped to anemia at age roband male 3.18 RPS26 Short stature secondary to allow for pubertal growth and 8.9 106 0.65 N/A N/A 3 months steroids then transfusion dependent bilaterally absent thumbs, small & fused radius/ulna; cardiac roband female 6.00 RPL5 anemia at birth steroid responsive 13.4 88.8 2.82 N/A N/A septal defect unspecified, missing ribs, imperforate anus roband female 8.87 RPS19 anemia at birth mild epicanthal folds steroid responsive 12.1 99.1 1.7 3.2 52.2 anemia at age duplication of renal collecting roband male 1.89 RPS10 steroid responsive 10.2 90.5 1.83 N/A N/A 1 year system roband male 1.97 RPS17 anemia at age failure to thrive, neutropenia transfusion dependent 7.2 86 N/A N/A N/A file:///X:/jmedgenet/Issue%20makeup/jmedgenet_54_6/Supplement%20R2.htm 2/6 12/28/2018 Supplement R2.htm 2 months 10/10 MUD HSCT at age 3 for steroid refractory, transfusion roband male 0.73 RPS19 anemia at birth no dysmorphology reported 7.9 82.2 N/A N/A N/A dependent anemia and iron overload steroid responsive, then steroids anemia at age roband male 31.26 RPS19 no dysmorphology reported and transfusion dependent from 10.5 126 1.33 14.5 762 3 months age 31 years bilateral epicanthal folds, broad anemia at age fspring male 6.10 RPS19 nasal root, webbed neck, low steroid responsive 9.6 103 2.51 7.5 669 3 months posterior hairline, clinodactyly anemia at age roband male 42 RPS26 no dysmorphology reported steroid responsive N/A N/A N/A N/A N/A 2 months metopic suture ridge, microcephaly, large eyes, roband male 0.83 RPL35A anemia at birth transfusion dependent since birth 8.5 83.5 0.3 N/A N/A asymmetric ears, atrial septal defect †: Age at study entry ††: Treatment last reported †††: Results prior to red blood cell transfusion, when applicable VSD: ventricular septal defect; HSCT: hematopoietic stem cell transplant; MUD: matched unrelated donor; Hb: hemoglobin; MCV: mean corpuscular volume; eADA: erythrocyte adenosine deaminase level; HbF: fetal hemoglobin; epo: erythropoietin; N/A: not available Supplemental Table 6A. Genes deleted in family NCI-51 with large deletion involving ribosomal genes RPS17 and RPS17L Family NCI-51 Deletion chr15:82,993,199-84,790,612 (1,797,413 bp)* Gene Start position End position GOLGA6L10 83009406 83018198 UBE2Q2P2 83023772 83084341 UBE2Q2P3 83023772 83084729 GOLGA6L9 83098709 83108111 LOC440297 83130032 83145983 LOC727849 83140198 83182930 AGSK1 83140663 83182901 RPS17L** 83205503 83209208 RPS17** 83205503 83209208 CPEB1 83211950 83316728 LOC283692 83316520 83361572 AP3B2 83328032 83378635 LOC338963 83379222 83382745 LOC283693 83394649 83408532 SCARNA15 83424696 83424823 FSD2 83428023 83474806 WHAMM 83477972 83503613 HOMER2 83517728 83621476 FAM103A1 83654954 83659809 C15orf40 83657714 83680393 BTBD1 83685180 83736106 MIR4515 83736086 83736167 TM6SF1 83776323 83806111 HDGFRP3 83806803 83876770 BNC1 83924654 83953468 SH3GL3 84116090 84287493 ADAMTSL3 84322837 84708593 EFTUD1P1 84748938 84795353 *reported based on Genome Research Consortium GRCh37/hg19 assembly **Genes of interest Supplemental Table 6B. Genes deleted in family NCI-71 with large deletion involving ribosomal gene RPL35A Family NCI-71 Deletion chr3:195,507,436-198,022,430 (2,514,994 bp)* Gene Start position End position file:///X:/jmedgenet/Issue%20makeup/jmedgenet_54_6/Supplement%20R2.htm 3/6 12/28/2018 Supplement R2.htm MUC4 195473637 195538844 TNK2 195590235 195635880 SDHAP1 195686791 195717150 TFRC 195776154 195809032 LOC401109 195869506 195887761 ZDHHC19 195924322 195938300 SLC51A 195943382
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  • Identification of Novel DNA-Methylated Genes

    Identification of Novel DNA-Methylated Genes

    Prostate Cancer and Prostatic Disease (2013) 16, 292–300 & 2013 Macmillan Publishers Limited All rights reserved 1365-7852/13 www.nature.com/pcan ORIGINAL ARTICLE Identification of novel DNA-methylated genes that correlate with human prostate cancer and high-grade prostatic intraepithelial neoplasia JM Devaney1, S Wang2,3, S Funda1, J Long2, DJ Taghipour2, R Tbaishat3, P Furbert-Harris2,4, M Ittmann5 and B Kwabi-Addo2,3 BACKGROUND: Prostate cancer (PCa) harbors a myriad of genomic and epigenetic defects. Cytosine methylation of CpG-rich promoter DNA is an important mechanism of epigenetic gene inactivation in PCa. There is considerable amount of data to suggest that DNA methylation-based biomarkers may be useful for the early detection and diagnosis of PCa. In addition, candidate gene- based studies have shown an association between specific gene methylation and alterations and clinicopathologic indicators of poor prognosis in PCa. METHODS: To more comprehensively identify DNA methylation alterations in PCa initiation and progression, we examined the methylation status of 485 577 CpG sites from regions with a broad spectrum of CpG densities, interrogating both gene-associated and non-associated regions using the recently developed Illumina 450K methylation platform. RESULTS: In all, we selected 33 promoter-associated novel CpG sites that were differentially methylated in high-grade prostatic intraepithelial neoplasia and PCa in comparison with benign prostate tissue samples (false discovery rate-adjusted P-value o0.05; b-value X0.2; fold change 41.5). Of the 33 genes, hierarchical clustering analysis demonstrated BNC1, FZD1, RPL39L, SYN2, LMX1B, CXXC5, ZNF783 and CYB5R2 as top candidate novel genes that are frequently methylated and whose methylation was associated with inactivation of gene expression in PCa cell lines.
  • Noelia Díaz Blanco

    Noelia Díaz Blanco

    Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr.
  • Structural Variant Calling by Assembly in Whole Human Genomes: Applications in Hypoplastic Left Heart Syndrome by Matthew Kendzi

    Structural Variant Calling by Assembly in Whole Human Genomes: Applications in Hypoplastic Left Heart Syndrome by Matthew Kendzi

    STRUCTURAL VARIANT CALLING BY ASSEMBLY IN WHOLE HUMAN GENOMES: APPLICATIONS IN HYPOPLASTIC LEFT HEART SYNDROME BY MATTHEW KENDZIOR THESIS Submitted in partial FulFillment oF tHe requirements for the degree of Master of Science in BioinFormatics witH a concentration in Crop Sciences in the Graduate College of the University oF Illinois at Urbana-Champaign, 2019 Urbana, Illinois Master’s Committee: ProFessor MattHew Hudson, CHair ResearcH Assistant ProFessor Liudmila Mainzer ProFessor SaurabH SinHa ABSTRACT Variant discovery in medical researcH typically involves alignment oF sHort sequencing reads to the human reference genome. SNPs and small indels (variants less than 50 nucleotides) are the most common types oF variants detected From alignments. Structural variation can be more diFFicult to detect From short-read alignments, and thus many software applications aimed at detecting structural variants From short read alignments have been developed. However, these almost all detect the presence of variation in a sample using expected mate-pair distances From read data, making them unable to determine the precise sequence of the variant genome at the speciFied locus. Also, reads from a structural variant allele migHt not even map to the reference, and will thus be lost during variant discovery From read alignment. A variant calling by assembly approacH was used witH tHe soFtware Cortex-var for variant discovery in Hypoplastic Left Heart Syndrome (HLHS). THis method circumvents many of the limitations oF variants called From a reFerence alignment: unmapped reads will be included in a sample’s assembly, and variants up to thousands of nucleotides can be detected, with the Full sample variant allele sequence predicted.