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2014-Platform-Abstracts.Pdf American Society of Human Genetics 64th Annual Meeting October 18–22, 2014 San Diego, CA PLATFORM ABSTRACTS Abstract Abstract Numbers Numbers Saturday 41 Statistical Methods for Population 5:30pm–6:50pm: Session 2: Plenary Abstracts Based Studies Room 20A #198–#205 Featured Presentation I (4 abstracts) Hall B1 #1–#4 42 Genome Variation and its Impact on Autism and Brain Development Room 20BC #206–#213 Sunday 43 ELSI Issues in Genetics Room 20D #214–#221 1:30pm–3:30pm: Concurrent Platform Session A (12–21): 44 Prenatal, Perinatal, and Reproductive 12 Patterns and Determinants of Genetic Genetics Room 28 #222–#229 Variation: Recombination, Mutation, 45 Advances in Defining the Molecular and Selection Hall B1 Mechanisms of Mendelian Disorders Room 29 #230–#237 #5-#12 13 Genomic Studies of Autism Room 6AB #13–#20 46 Epigenomics of Normal Populations 14 Statistical Methods for Pedigree- and Disease States Room 30 #238–#245 Based Studies Room 6CF #21–#28 15 Prostate Cancer: Expression Tuesday Informing Risk Room 6DE #29–#36 8:00pm–8:25am: 16 Variant Calling: What Makes the 47 Plenary Abstracts Featured Difference? Room 20A #37–#44 Presentation III Hall BI #246 17 New Genes, Incidental Findings and 10:30am–12:30pm:Concurrent Platform Session D (49 – 58): Unexpected Observations Revealed 49 Detailing the Parts List Using by Exome Sequencing Room 20BC #45–#52 Genomic Studies Hall B1 #247–#254 18 Type 2 Diabetes Genetics Room 20D #53–#60 50 Statistical Methods for Multigene, 19 Genomic Methods in Clinical Practice Room 28 #61–#68 Gene Interaction and Pathway 20 Genetics and Mechanisms in Analyses Room 6AB #255–#262 Neurological Disorders Room 29 #69–#76 51 Neurogenetics: From Gene to 21 Developmental Genetics: Mechanism Room 6CF #263–#270 Immunodeficiencies and Autoimmune 52 Contribution of Common and Rare Disorders Room 30 #77–#84 Variation to Obesity-Related Traits Room 6DE #271–#278 53 The Dynamic Genome: Structural Monday and Somatic Variation Room 20A #279–#286 8:00pm–8:25am: 54 Expanding Clinical Phenotypes Room 20BC #287–#294 22 Plenary Abstracts Featured 55 Cancer Susceptibility Genes: Presentation II Hall BI #85 Identification and Implementation Room 20D #295–#302 10:30am–12:30pm: Concurrent Platform Session B (27 – 36): 56 Balanced and Unbalanced 27 Cloudy with a Chance of Big Data Hall B1 #86–#93 Chromosomal Rearrangements Room 28 #303–#310 28 Architecture and Impact of Human 57 Diagnostic Yield of New Genomic Knockout Alleles Room 6AB #94–#101 Technologies Room 29 #311–#318 29 Population Structure, Admixture, and 58 Genetic/Genomic Education and Human History Room 6CF #102–#109 Services Delivery Room 30 #319–#326 30 Neurogenetics: From Gene to 4:30pm–6:30pm: Concurrent Platform Session E (59–68): Mechanism Room 6DE #110–#117 59 We Have the Technology: 31 Cardiovascular Genetics I: Single Next-Generation Genomic Methods Room 6AB #327–#334 Gene Stories Room 20A #118–#125 60 Hereditary Breast-Ovarian Cancer Room 6CF #335–#342 32 Molecular Insights into Mendelian 61 Genomic Studies of Schizophrenia Disorders Room 20BC #126–#133 and Bipolar Disorder Room 6DE #343–#350 33 Genomic Alterations of Tumors Room 20D #134–#141 62 From Association to Function in 34 Metabolic Disorders: New Diagnostics Complex Traits Room 20A #351–#358 and Pathogenic Insights Room 28 #142–#149 63 Therapy for Genetic Disorders Room 20BC #359–#366 35 Looking between the Streetlamps: 64 Exome Sequencing as Standard of Variant Phasing and Imputation Room 29 #150–#157 Care in Clinical Genetics Room 20D #367–#374 36 Chromatin, Gene Regulation and 65 Beyond the Sequence: Genomic Expression Room 30 #158–#165 Regulation and Disease Room 28 #375–#382 4:30pm–6:30pm: Concurrent Platform Session C (37–46): 66 A Clear Vision for Genetic Eye 37 From Bytes To Phenotypes Hall B1 #166–#173 Diseases Room 29 #383–#390 38 Rare Mutations, Well Done Room 6AB #174–#181 67 Autoimmune Genes: Discovery & 39 Cardiovascular Genetics II: Genetic Function Room 30 #391–#398 Discovery and Characterization Room 6CF #182–#189 68 Pharmacogenetics: From Association 40 Genetics of Complex Neuropsychiatric to Action Room 6AB #398–#406 Disorders Room 6DE #190–#197 Copyright © 2014 The American Society of Human Genetics. All rights reserved. X : 52528$PLCV 09-13-14 02:32:35 Layout: 30917X : Start Odd Page 1 ASHG 2014 Abstracts 1 1 2 The UK10K project: rare variants in health and disease. N. Soranzo, Human-specific gene evolution and structural diversity of the chromo- The UK10K Consortium. Wellcome Trust Sanger Institute, Cambridge, some 16p11.2 autism CNV. X. Nuttle1, G. Giannuzzi2, M.H. Duyzend1, United Kingdom. P.H. Sudmant1, O. Penn1, G. Chiatante3, M. Malig1, J. Huddleston1,4, L. Understanding of how genetic variation contributes to human traits and Denman1, L. Harshman1, C. Baker1, A. Raja1,4, K. Penewit1, F. Antonacci3, which genes are involved is still largely incomplete. Rare and low frequency R. Bernier5, A. Reymond2, E.E. Eichler1,4. 1) Department of Genome Sci- genetic variants (defined as minor allele frequency [MAF] <1% and 1-5%, ences, University of Washington School of Medicine, Seattle, WA, USA; 2) respectively) are thought to play a role in common and rare disease, but Center for Integrative Genomics, University of Lausanne, Lausanne, Switz- until recently it has not been possible to assess their contribution systemati- erland; 3) Department of Biology. University of Bari, Bari, Italy; 4) Howard cally. The UK10K project (www.uk10k.org) studies the contribution rare Hughes Medical Institute, Seattle, WA, USA; 5) Department of Psychiatry, and low frequency variation to a wide spectrum of biomedically relevant University of Washington, Seattle, WA, USA. quantitative traits and diseases with different predicted genetic architecture. Recurrent deletions and duplications at 16p11.2 are a major contributor Here we describe the data generated by the different arms of the UK10K to autism and also associate with schizophrenia and extremes of body project, and use it to address empirically important open questions. We mass index and head circumference. These events occur via nonallelic show that the 24 million novel genetic variants identified provide an extensive homologous recombination (NAHR) between directly oriented segmental reference genetic sample for the UK, with fewer than 10% rare variants duplications (BP4 and BP5) ~600 kbp apart. Using whole genome sequenc- shared with other large scale resources. The resulting haplotype panel ing (WGS) data from 2,551 humans, 86 great apes, a Neanderthal, and a boosts accuracy and coverage of imputation of rare variants in GWAS Denisovan, we observed extensive copy number variation in BP4 and BP5 studies. We discuss the value of these data for discovery and interpretation in human populations and identified BOLA2 as a gene duplicated in Homo of variants of clinical importance, including an evaluation of incidental find- sapiens after our divergence from ancient hominins. Performing massively ings that suggests that greater than 5% participants carry rare and potentially parallel and PacBio sequencing of large-insert clones from orangutan and actionable genetic variants. We describe how demographic history influ- chimpanzee, we generated complete sequence over the 16p11.2 locus in ences the observed weak structuring of rare variation in the UK (MAF= these apes and reconstructed its evolutionary history. We find three inver- 0.1-0.3%), and evaluate empirically the potential for confounding due to sions occurred in the human lineage after divergence from orangutan, affect- stratification in association studies of complex traits. We describe the contri- ing > 1 Mbp of sequence, including 45 genes. In concert with these evolution- bution of common, low frequency and rare variants to 61 biomedically impor- ary inversions, > 950 kbp have been added to the region via segmental tant quantitative traits, describing novel alleles associated with adiponectin duplication. Comparative sequence analyses suggest that BOLA2 was part (ADPOQ), lipids (PCSK9, LPL, APOC3|APOA4|APOA1, PCSK7, CETP, of an ~110 kbp segment that duplicated from BP5 to BP4 ~250 kya at the LIPG, LDLR and APOE) and several other traits. We further discuss general time when Homo sapiens emerged as a species. Modern humans carry at characteristics of rare variant associations from the comparative evaluation least one additional copy of BOLA2 (ranging from 3 to 14 diploid copies) in of the allelic architecture of the 61 traits. The data released to the scientific contrast to apes, Neanderthal, and Denisova, where the gene exists as two community includes individual-level genotypic and phenotypic data, a refer- diploid copies. BOLA2 is thought to be involved in cell proliferation or cell ence panel of haplotypes for imputation of rare variants into genome-wide cycle regulation. RT-PCR and RNA-seq suggest BOLA2 is widely expressed, SNP arrays and analysis protocols and summary results for complex trait and expression levels in lymphoblastoid cell lines correlate with copy number associations based on single-marker and rare variant aggregation tests. Our (r = 0.29). Using the same sequencing strategy as above, we completely results inform future whole-genome and whole-exome sequencing based sequenced four distinct human structural haplotypes at 16p11.2 (> 5 Mbp studies seeking to characterize the role of rare genetic variation in predisposi- of sequence). We discover haplotypes where BP4 and BP5 differ by tion to rare and common disease. hundreds of kbp including tandem duplications of BOLA2, leading to likely differences in predisposition to NAHR. Leveraging our high quality human haplotype sequences, we are currently assaying BOLA2 copy number and refining breakpoints in > 125 patients with a 16p11.2 deletion or duplication. Our preliminary data suggest that breakpoints cluster near the Homo sap- iens-specific duplications involving BOLA2. These findings raise the exciting possibility that predisposition to recurrent rearrangements associated with autism is linked to the emergence of novel duplicated genes in the last 250,000 years of our species' evolution.
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