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David Altshuler

Bio: David Altshuler is an academic researcher from University of Michigan. The author has contributed to research in topics: Genome-wide association study & Population. The author has an hindex of 162, co-authored 345 publications receiving 201782 citations. Previous affiliations of David Altshuler include Vertex Pharmaceuticals & Massachusetts Institute of Technology.


Papers
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Journal ArticleDOI
TL;DR: Evidence is provided that genetic variation among MODY genes may influence response to insulin-sensitizing interventions, and an aggregate of rare missense variants and insulinogenic traits is examined.
Abstract: Context: Variation in genes that cause maturity-onset diabetes of the young (MODY) has been associated with diabetes incidence and glycemic traits. Objectives: This study aimed to determine whether genetic variation in MODY genes leads to differential responses to insulin-sensitizing interventions. Design and Setting: This was a secondary analysis of a multicenter, randomized clinical trial, the Diabetes Prevention Program (DPP), involving 27 US academic institutions. We genotyped 22 missense and 221 common variants in the MODY-causing genes in the participants in the DPP. Participants and Interventions: The study included 2806 genotyped DPP participants randomized to receive intensive lifestyle intervention (n = 935), metformin (n = 927), or placebo (n = 944). Main Outcome Measures: Association of MODY genetic variants with diabetes incidence at a median of 3 years and measures of 1-year β-Cell function, insulinogenic index, and oral disposition index. Analyses were stratified by treatment group for significant single-nucleotide polymorphism 3 treatment interaction (Pint, 0.05). Sequence kernel association tests examined the association between an aggregate of rare missense variants and insulinogenic traits. Results: After 1 year, the minor allele of rs3212185 (HNF4A) was associated with improved β-Cell function in the metformin and lifestyle groups but not the placebo group; the minor allele of rs6719578 (NEUROD1) was associated with an increase in insulin secretion in the metformin group but not in the placebo and lifestyle groups. Conclusions: These results provide evidence that genetic variation among MODY genes may influence response to insulin-sensitizing interventions.

13 citations

Posted ContentDOI
31 Jul 2018-bioRxiv
TL;DR: An exome sequence analysis of type 2 diabetes cases and controls presents a Bayesian framework to recalibrate association p-values as posterior probabilities of association, estimating that reaching p<0.05 in this study increases the odds of causal T2D association for a nonsynonymous variant by a factor of 1.3.
Abstract: Protein-coding genetic variants that strongly affect disease risk can provide important clues into disease pathogenesis. Here we report an exome sequence analysis of 20,791 type 2 diabetes (T2D) cases and 24,440 controls from five ancestries. We identify rare (minor allele frequency 30 SLC30A8 alleles, and (b) within 12 gene sets, including those corresponding to T2D drug targets (p=6.1×10-3) and candidate genes from knockout mice (p=5.2×10-3). Within our study, the strongest T2D rare variant gene-level signals explain at most 25% of the heritability of the strongest common single variant signals, and the rare variant gene-level effect sizes we observe in established T2D drug targets will require 110K-180K sequenced cases to exceed exome-wide significance. To help prioritize genes using associations from current smaller sample sizes, we present a Bayesian framework to recalibrate association p-values as posterior probabilities of association, estimating that reaching p

13 citations

Journal ArticleDOI
TL;DR: Delayed failures of structural augmentation with cement during kyphoplasty do occur and can lead to additional surgeries, and a possible predictive index may include wall integrity of the vertebral body, competency of the posterior tension band, and location of the kyPHoplasty at a junctional spinal level.
Abstract: OBJECT Pathological compression fractures in cancer patients cause significant pain and disability. Spinal metastases affect quality of life near the end of life and may require multiple procedures, including medical palliative care and open surgical decompression and fixation. An increasingly popular minimally invasive technique to treat metastatic instabilities is kyphoplasty. Even though it may alleviate pain due to pathological fractures, it may fail. However, delayed kyphoplasty failures with retropulsed cement and neural element compression have not been well reported. Such failures necessitate open surgical decompression and stabilization, and cement inserted during the kyphoplasty complicates salvage surgeries in patients with a disease-burdened spine. The authors sought to examine the incidence of delayed failure of structural kyphoplasty in a series of cement augmentations for pathological compression fractures. The goal was to identify risk predictors by analyzing patient and disease characteristics to reduce kyphoplasty failure and to prevent excessive surgical procedures at the end of life. METHODS The authors retrospectively reviewed the records of all patients with metastatic cancer from 2010 to 2013 who had undergone a procedure involving cement augmentation for a pathological compression fracture at their institution. The authors examined the characteristics of the patients, diseases, and radiographic fractures. RESULTS In total, 37 patients underwent cement augmentation in 75 spinal levels during 45 surgeries. Four patients had delayed structural kyphoplasty failure necessitating surgical decompression and fusion. The mean time to kyphoplasty failure was 2.88 ± 1.24 months. The mean loss of vertebral body height was 16% in the patients in whom kyphoplasty failed and 32% in patients in whom kyphoplasty did not fail. No posterior intraoperative cement extravasation was observed in the patients in whom kyphoplasty had failed. The mean spinal instability neoplastic score was 10.8 in the patients in whom kyphoplasty failed and 10.1 in those in whom kyphoplasty did not fail. Approximately 50% of the kyphoplasty failures occurred at junctional spinal levels. All the patients in whom kyphoplasty failed had fractures in 3 or more cortical walls before treatment, whereas 46% of patients in the nonfailure group had fractures with breaching of 3 or more walls. CONCLUSIONS Although rare, delayed failures of structural augmentation with cement during kyphoplasty do occur and can lead to additional surgeries. A possible predictive index may include wall integrity of the vertebral body, competency of the posterior tension band, and location of the kyphoplasty at a junctional spinal level. Additional studies are required to confirm these findings.

12 citations

Patent
04 Dec 2006
TL;DR: In this article, methods for predicting the immunocompatibility of two subjects that include determining the presence or absence of one or more deletion variants in the DNA sequence of a gene, where the deletion variant substantially prevents expression of the protein encoded by the gene.
Abstract: Disclosed herein are methods for predicting the immunocompatibility of two subjects that include determining the presence or absence of one or more deletion variants in the DNA sequence of a gene, where the deletion variant substantially prevents expression of the protein encoded by the gene.

12 citations

Journal ArticleDOI
27 May 2004-Nature
TL;DR: Genome sequence data are enabling clinical genomic investigation, in which the characteristics of human patients are explored using comprehensive inventories of biomolecules, and projects will increasingly rely on fully integrated multidisciplinary teams, demanding new organizational models in academic biomedical research.
Abstract: Genome sequence data are enabling clinical genomic investigation, in which the characteristics of human patients are explored using comprehensive inventories of biomolecules. Successful investigators must navigate rapid technological change, collect and analyse large volumes of data, and engage systems of clinical care. Such projects will increasingly rely on fully integrated multidisciplinary teams, demanding new organizational models in academic biomedical research.

12 citations


Cited by
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Journal ArticleDOI
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Abstract: As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

37,898 citations

Journal ArticleDOI
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Abstract: Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.

34,830 citations

Journal ArticleDOI
TL;DR: This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
Abstract: Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.

26,280 citations

Journal ArticleDOI
Eric S. Lander1, Lauren Linton1, Bruce W. Birren1, Chad Nusbaum1  +245 moreInstitutions (29)
15 Feb 2001-Nature
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

22,269 citations

Journal ArticleDOI
TL;DR: The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
Abstract: limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.

22,147 citations