Adam Felsenfeld

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Completing the map of human genetic variation

Large-scale studies of human genetic variation have focused largely on understanding the pattern and nature of single-nucleotide differences within the human genome. Recent studies that have identified larger polymorphisms, such as insertions, deletions and inversions, emphasize the value of investing in more comprehensive and systematic studies of human structural genetic variation. We describe a community resource project recently launched by the National Human Genome Research Institute (NHGRI) to sequence large-insert clones from many individuals, systematically discovering and resolving these complex variants at the DNA sequence level. The project includes the discovery of variants through development of clone resources, sequence resolution of variants, and accurate typing of variants in individuals of African, European or Asian ancestry. Sequence resolution of both single-nucleotide and larger-scale genomic variants will improve our picture of natural variation in human populations and will enhance our ability to link genetics and human health.

ALZHEIMER'S DISEASE SEQUENCING PROJECT: SEARCH FOR ALZHEIMER'S DISEASE RESILIENCE GENES THAT MAY MODIFY DISEASE SUSCEPTIBILITY IN SPECIFIC APOE GENOTYPE BACKGROUNDS

not available. EC-01-04 PHYSIOLOGICAL SUBSTRATES OF BACE1 AND ADAM10: SAFETY ISSUES OR BIOMARKERS? Stefan Lichtenthaler, Technical University of Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.. Contact e-mail: Stefan.Lichtenthaler@dzne.de Background: The beta-secretase BACE1 is a major drug target in Alzheimer’s disease (AD), but also has other functions, e.g. in myelination and axon targeting. BACE1-deficient mice have additional phenotypes in the brain and several BACE1 substrates, referred to as the BACE1 degradome, are emerging in the CNS. This raises the possibility that therapeutic BACE1 inhibition may have mechanism-based side-effects. Additionally, most BACE1 inhibitors also block the homologous protease BACE2 and, thus, may interfere with BACE2 function. Methods: We developed methods for whole proteome analysis of murine tissue, including CSF Results: We used the novel methods to identify BACE1 substrate candidates in murine CSF, but also in neurons and brains. Selected substrate candidates were validated and functionally and mechanistically characterized. Two of the candidates are seizure protein 6 (SEZ6) and SEZ6-like (SEZ6L), which control neurite outgrowth and synapse formation. Both proteins were validated as BACE1 substrates in vitro and in vivo. In CSF, SEZ6 and SEZ6Lwere found to be suitable markers for measuring BACE1 inhibition in vivo. Conclusions: BACE1 has broad functions in the CNS. The presentation will discuss the implication of the substrates a) for the safety of BACE1 inhibitors and b) for the use as companion diagnostics to monitor BACE inhibition in vivo. SUNDAY, JULY 24, 2016 FEATURED RESEARCH SESSIONS F1-01 THE ALZHEIMER’S DISEASE SEQUENCING PROJECT (ADSP): GENE DISCOVERY IN ACTION F1-01-01 STRUCTURALVARIATION (SV) IN HETEROGENOUS WHOLE-GENOME SEQUENCING DATA FROM 111 FAMILIES AT RISK FOR ALZHEIMER DISEASE: ALZHEIMER DISEASE SEQUENCING PROJECT SV STUDY Li Charlie Xia, Stanford University, Stanford, CA, USA; University of Pennsylvania, Philadelphia, PA, USA. Contact e-mail: lixia@stanford.edu Background: The Alzheimer Disease Sequencing Project (ADSP) is a national initiative to identify novel genetic variants involved in determining risk of late-onset Alzheimer disease (AD). Methods: Structural variation was characterized in 111 families of multiple ethnicities comprising 578 individuals diagnosed with or at risk for AD. We developed a statistical framework that leverages pedigree information to assess accuracy and optimize structural variant (SV) calls. The kinship coefficient was used to filter SVs showing excess heterozygosity. We also formulated a metric called the D-score which is an outgroup-based measure of sib-sharing to filter SVs identified by calling algorithms that detect insertion and deletion breakpoints, but do not render genotypes. These metrics also permitted assessment of reliability of individual calling programs for various SV sizes. An in silico procedure was devised to “spike-in” SVs of varying purity into real sequenced libraries, accommodating multi-library designs, and applied it to three samples that were sequenced at all three centers. This comprehensive QC process allowed benchmarking SV callers across the widely differing libraries and combining these callers in a library-specific way for improved specificity and sensitivity. Candidate SV regions were further refined using an ensemble of 12 SV callers with local assembly to provide precise breakpoints for subsequent calling of genotypes. Results:We identified a high-confidence set of deletions, insertions, and complex variants larger than 20 base pairs (bp) genotyped across all 578 individuals. These variants were prioritized based on predicted functional impact and overlap with known AD genes and linkage regions. Thus far, we detected, and confirmed by sequencing, a 44 bp ABCA7 deletion in 11 members (all have AD) of 5 of 67 CaribbeanHispanic families. This finding is consistent with our recent AD association finding of this deletion in a sample containing >2,800 African Americans which results in a frameshift and truncating mutation that could interfere with protein function. Conclusions: A carefully developed pipeline for detecting, genotyping, and filtering SVs from family-based whole genome sequence data permitted discovery of a robust association of AD risk with a rare 44 bp deletion in ABCA7. Amore comprehensive analysis of these data is underway. F1-01-02 ALZHEIMER’S DISEASE SEQUENCING PROJECT: SEARCH FOR ALZHEIMER’S DISEASE RESILIENCE GENES THAT MAY MODIFY DISEASE SUSCEPTIBILITY IN SPECIFIC APOE GENOTYPE BACKGROUNDS Eduardo Marcora, Alan E. Renton, Gary W. Beecham, Eric Boerwinkle, Laura Cantwell, Carlos Cruchaga, Rebecca Cweibel, Adam Felsenfeld, Myriam Fornage, Manav Kapoor, Keoni Kauwe, Mugdha Khaladkar, Dan Kobolt, Yiyi Ma, Richard Mayeux, Marilyn Miller, Adam C. Naj, Amanda B. Partch, Margaret A. Pericak-Vance, Gerard D. Schellenberg, Sudha Seshadri, Badri N. Vardarajan, Li-San Wang, Joshua C. Bis, Lindsay A. Farrer, Alison M. Goate, 1 Icahn School of Medicine at Mount Sinai, New York, NY, USA; 2 University of Miami Miller School of Medicine, Miami, FL, USA; Baylor College of Medicine, Houston, TX, USA; University of Texas Health Science Center at Houston, Houston, TX, USA; 5 University of Pennsylvania, Philadelphia, PA, USA; 6 Washington University in St. Louis, Saint Louis, MO, USA; Washington University School of Medicine, St. Louis, MO, USA; Knight Alzheimer Disease Center, St. Louis, MO, USA; Division of Genome Sciences, National HumanGenome Research Institute, Bethesda,MD, USA; 10 University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA; Brigham Young University, Provo, UT, USA; Washington University in St. Louis, St. Louis, MO, USA; Washington University, St. Louis, MO, USA; 14 The Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; Boston University, Boston, MA, USA; Columbia University, New York, NY, USA; Division of Neuroscience, National Institute on Aging, Bethesda, MD, USA; 18 University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA; Boston University School of Medicine, Boston, MA, USA; 21 University of Washington, Seattle, WA, USA. Contact e-mail: edoardo.marcora@mssm.edu Background:Common variation at the APOE locus is the strongest known genetic risk factor for Alzheimer’s disease (AD). Podium Presentations: Sunday, July 24, 2016 P162