(Q52560100)

3 May 2018

title

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. (English)

1 reference

3 May 2018

main subject

autism spectrum disorder

0 references

whole genome sequencing

1 reference

1

1 reference

3 May 2018

Aaron R Quinlan

42

1 reference

3 May 2018

Michael E. Talkowski

46

1 reference

3 May 2018

Ryan L Collins

Ryan L Collins

7

0 references

Lambertus Klei

23

Lambertus Klei

1 reference

3 May 2018

34

Nenad Sestan

1 reference

3 May 2018

Mark Joseph Daly

40

Mark J Daly

1 reference

3 May 2018

Joseph Buxbaum

39

Joseph D Buxbaum

1 reference

3 May 2018

Tomasz Nowakowski

25

Tomasz J Nowakowski

1 reference

3 May 2018

Arnold Kriegstein

32

Arnold R Kriegstein

1 reference

3 May 2018

Benjamin M. Neale

36

Benjamin M Neale

1 reference

3 May 2018

Eirene Markenscoff-Papadimitriou

10

Eirene Markenscoff-Papadimitriou

1 reference

3 May 2018

Clif Duhn

17

Clif Duhn

1 reference

3 May 2018

Sirisha Pochareddy

27

Sirisha Pochareddy

1 reference

3 May 2018

Jeffrey D Mandell

24

Jeffrey D Mandell

1 reference

3 May 2018

Kathryn Roeder

44

Kathryn Roeder

1 reference

3 May 2018

Hilary Coon

37

Hilary Coon

1 reference

3 May 2018

Harold Z Wang

13

Harold Z Wang

1 reference

3 May 2018

Louw Smith

28

Louw Smith

1 reference

3 May 2018

author name string

Harrison Brand

2

1 reference

3 May 2018

Joon-Yong An

3

1 reference

3 May 2018

Matthew R Stone

4

1 reference

3 May 2018

Lingxue Zhu

5

1 reference

3 May 2018

Joseph T Glessner

6

1 reference

3 May 2018

Shan Dong

8

1 reference

3 May 2018

Ryan M Layer

9

1 reference

3 May 2018

Andrew Farrell

11

1 reference

3 May 2018

Grace B Schwartz

12

1 reference

3 May 2018

Benjamin B Currall

14

1 reference

3 May 2018

Xuefang Zhao

15

1 reference

3 May 2018

Jeanselle Dea

16

1 reference

3 May 2018

Carolyn A Erdman

18

1 reference

3 May 2018

Michael C Gilson

19

1 reference

3 May 2018

Rachita Yadav

20

1 reference

3 May 2018

Robert E Handsaker

21

1 reference

3 May 2018

Seva Kashin

22

1 reference

3 May 2018

Yuwen Liu

26

1 reference

3 May 2018

Michael F Walker

29

1 reference

3 May 2018

Matthew J Waterman

30

1 reference

3 May 2018

Xin He

31

1 reference

3 May 2018

John L Rubenstein

33

1 reference

3 May 2018

Steven A McCarroll

35

1 reference

3 May 2018

A Jeremy Willsey

38

1 reference

3 May 2018

Matthew W State

41

1 reference

3 May 2018

Gabor T Marth

43

1 reference

3 May 2018

Bernie Devlin

45

1 reference

3 May 2018

Stephan J Sanders

47

1 reference

3 May 2018

language of work or name

English

0 references

publication date

26 April 2018

1 reference

3 May 2018

published in

Nature Genetics

1 reference

3 May 2018

https://scigraph.springernature.com/pub.10.1038/s41588-018-0107-y

exact match

0 references

cites work

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7 September 2018

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Genomic Patterns of De Novo Mutation in Simplex Autism.

7 September 2018

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7 September 2018

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No Evidence That Schizophrenia Candidate Genes Are More Associated With Schizophrenia Than Noncandidate Genes.

7 September 2018

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7 September 2018

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Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome

7 September 2018

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Prevalence and architecture of de novo mutations in developmental disorders

7 September 2018

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Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.

7 September 2018

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The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

7 September 2018

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Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

7 September 2018

1 reference

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The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

7 September 2018

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The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies.

7 September 2018

1 reference

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Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia

7 September 2018

1 reference

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Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

7 September 2018

1 reference

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Analysis of protein-coding genetic variation in 60,706 humans

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

7 September 2018

1 reference

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Wham: Identifying Structural Variants of Biological Consequence

7 September 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

7 September 2018

The PsychENCODE project

1 reference

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An integrated map of structural variation in 2,504 human genomes

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Evaluating historical candidate genes for schizophrenia

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Integrative analysis of 111 reference human epigenomes

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

From trans to cis: transcriptional regulatory networks in neocortical development

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Whole-genome sequencing of quartet families with autism spectrum disorder

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Large multiallelic copy number variations in humans

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

A Bayesian framework for de novo mutation calling in parents-offspring trios

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

A genome-wide association study of autism using the Simons Simplex Collection: Does reducing phenotypic heterogeneity in autism increase genetic homogeneity?

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

The contribution of de novo coding mutations to autism spectrum disorder

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Biological insights from 108 schizophrenia-associated genetic loci

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Toward better understanding of artifacts in variant calling from high-coverage samples

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

LUMPY: a probabilistic framework for structural variant discovery.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

An atlas of active enhancers across human cell types and tissues

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

A polygenic burden of rare disruptive mutations in schizophrenia

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

DeNovoGear: de novo indel and point mutation discovery and phasing.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Fecundity of patients with schizophrenia, autism, bipolar disorder, depression, anorexia nervosa, or substance abuse vs their unaffected siblings.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

DELLY: structural variant discovery by integrated paired-end and split-read analysis

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

GENCODE: the reference human genome annotation for The ENCODE Project

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Rate of de novo mutations and the importance of father's age to disease risk

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Patterns and rates of exonic de novo mutations in autism spectrum disorders

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Topological domains in mammalian genomes identified by analysis of chromatin interactions

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

ChromHMM: automating chromatin-state discovery and characterization

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Characterization of the proteome, diseases and evolution of the human postsynaptic density.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

The Simons Simplex Collection: a resource for identification of autism genetic risk factors

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Hi-C: a method to study the three-dimensional architecture of genomes

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

BEDTools: a flexible suite of utilities for comparing genomic features

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Detection of nonneutral substitution rates on mammalian phylogenies

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

ChIP-seq accurately predicts tissue-specific activity of enhancers

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Why Most Discovered True Associations Are Inflated

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Estimation of significance thresholds for genomewide association scans

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

VISTA Enhancer Browser--a database of tissue-specific human enhancers

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Genome-wide association studies for common diseases and complex traits

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

The human genome browser at UCSC

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

Sequential Translation of Trinucleotide Codons for the Initiation and Termination of Protein Synthesis

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5961723

10.1038/S41588-018-0107-Y

7 September 2018

Identifiers

DOI

1 reference

3 May 2018

PMC publication ID

5961723

0 references

1 reference

3 May 2018