Recent ultra-rare inherited variants implicate new autism candidate risk genes

Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

(2020) F. Kyle Satterstrom et al.   CELL

Identification of common genetic risk variants for autism spectrum disorder

(2019) Jakob Grove et al.   NATURE GENETICS

Nonrandom occurrence of multiple de novo coding variants in a proband indicates the existence of an oligogenic model in autism

(2019) Yaoqiang Du et al.   GENETICS IN MEDICINE

Ultra-Rare Genetic Variation in the Epilepsies: A Whole-Exome Sequencing Study of 17,606 Individuals

(2019) Yen-Chen Anne Feng et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

(2019) Elizabeth K. Ruzzo et al.   CELL

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

A method for genome-wide genealogy estimation for thousands of samples

(2019) Leo Speidel et al.   NATURE GENETICS

Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes

(2019) Pamela Feliciano et al.   npj Genomic Medicine

Autism spectrum disorder and attention deficit hyperactivity disorder have a similar burden of rare protein-truncating variants

(2019) F. Kyle Satterstrom et al.   NATURE NEUROSCIENCE

Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes

(2019) PingHsun Hsieh et al.   SCIENCE

Sex-Based Analysis of De Novo Variants in Neurodevelopmental Disorders

(2019) Tychele N. Turner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Quantifying the Impact of Rare and Ultra-rare Coding Variation across the Phenotypic Spectrum

(2018) Andrea Ganna et al.   AMERICAN JOURNAL OF HUMAN GENETICS

De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder

(2018) Lot Snijders Blok et al.   HUMAN GENETICS

SPARK: A US Cohort of 50,000 Families to Accelerate Autism Research

(2018) Pamela Feliciano et al.   NEURON

Neurobeachin and the Kinesin KIF21B Are Critical for Endocytic Recycling of NMDA Receptors and Regulate Social Behavior

(2018) Kira V. Gromova et al.   Cell Reports

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

(2018) Allison A. Regier et al.   Nature Communications

Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes

(2018) Hui Guo et al.   GENETICS IN MEDICINE

Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity

(2018) Bradley P. Coe et al.   NATURE GENETICS

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

(2018) Joon-Yong An et al.   SCIENCE

A de novo dominant mutation in KIF1A associated with axonal neuropathy, spasticity and autism spectrum disorder

(2017) Pedro J. Tomaselli et al.   JOURNAL OF THE PERIPHERAL NERVOUS SYSTEM

Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

(2017) Daniel J Weiner et al.   NATURE GENETICS

Genetics of early-onset Parkinson's disease in Finland: exome sequencing and genome-wide association study

(2017) Ari Siitonen et al.   NEUROBIOLOGY OF AGING

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

(2016) Tychele N. Turner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Excess of rare, inherited truncating mutations in autism

(2015) Niklas Krumm et al.   NATURE GENETICS

Large multiallelic copy number variations in humans

(2015) Robert E Handsaker et al.   NATURE GENETICS

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

(2015) Stephan J. Sanders et al.   NEURON

Low load for disruptive mutations in autism genes and their biased transmission

(2015) Ivan Iossifov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global diversity, population stratification, and selection of human copy-number variation

(2015) Peter H. Sudmant et al.   SCIENCE

Wham: Identifying Structural Variants of Biological Consequence

(2015) Zev N. Kronenberg et al.   PLoS Computational Biology

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Using theRPackagecrlmmfor Genotyping and Copy Number Estimation

(2015) Robert B. Scharpf et al.   Journal of Statistical Software

Novel Carboxypeptidase A6 (CPA6) Mutations Identified in Patients with Juvenile Myoclonic and Generalized Epilepsy

(2015) Matthew R. Sapio et al.   PLoS One

Variations in the FRA10AC1 Fragile Site and 15q21 Are Associated with Cerebrospinal Fluid Aβ1-42 Level

(2015) Qingqin S. Li et al.   PLoS One

Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders

(2014) Dalila Pinto et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Genotype-First Approach to Defining the Subtypes of a Complex Disease

(2014) Holly A. Stessman et al.   CELL

Disruptive CHD8 Mutations Define a Subtype of Autism Early in Development

(2014) Raphael Bernier et al.   CELL

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

A framework for the interpretation of de novo mutation in human disease

(2014) Kaitlin E Samocha et al.   NATURE GENETICS

Most genetic risk for autism resides with common variation

(2014) Trent Gaugler et al.   NATURE GENETICS

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

The Autism Simplex Collection: an international, expertly phenotyped autism sample for genetic and phenotypic analyses

(2014) Joseph D Buxbaum et al.   Molecular Autism

Rare-Variant Extensions of the Transmission Disequilibrium Test: Application to Autism Exome Sequence Data

(2013) Zongxiao He et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Topoisomerases facilitate transcription of long genes linked to autism

(2013) Ian F. King et al.   NATURE

Integrated Model of De Novo and Inherited Genetic Variants Yields Greater Power to Identify Risk Genes

(2013) Xin He et al.   PLoS Genetics

Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth

(2012) Menachem Fromer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2012) T. Rausch et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Copy number variation detection and genotyping from exome sequence data

(2012) N. Krumm et al.   GENOME RESEARCH

Autism recurrence in half siblings: strong support for genetic mechanisms of transmission in ASD

(2012) J N Constantino et al.   MOLECULAR PSYCHIATRY

HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle

(2012) Matthew A. Deardorff et al.   NATURE

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

(2012) Brian J. O’Roak et al.   NATURE

Phenotypic Heterogeneity of Genomic Disorders and Rare Copy-Number Variants

(2012) Santhosh Girirajan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

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

(2011) H. Li   BIOINFORMATICS

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

(2011) A. Abyzov et al.   GENOME RESEARCH

Oligogenic heterozygosity in individuals with high-functioning autism spectrum disorders

(2011) C. P. Schaaf et al.   HUMAN MOLECULAR GENETICS

Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism

(2011) Stephan J. Sanders et al.   NEURON

Demographic history and rare allele sharing among human populations

(2011) S. Gravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Haploinsufficiency of HDAC4 Causes Brachydactyly Mental Retardation Syndrome, with Brachydactyly Type E, Developmental Delays, and Behavioral Problems

(2010) Stephen R. Williams et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay

(2010) Santhosh Girirajan et al.   NATURE GENETICS

The Simons Simplex Collection: A Resource for Identification of Autism Genetic Risk Factors

(2010) Gerald D. Fischbach et al.   NEURON

Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells

(2010) Joseph D. Dougherty et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Autism genome-wide copy number variation reveals ubiquitin and neuronal genes

(2009) Joseph T. Glessner et al.   NATURE

Polarized Targeting of Neurexins to Synapses Is Regulated by their C-Terminal Sequences

(2008) R. Fairless et al.   JOURNAL OF NEUROSCIENCE