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Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism

A. Jeremy Willsey, +37 more
- 21 Nov 2013 - 
- Vol. 155, Iss: 5, pp 997-1007
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TLDR
Coexpression networks are constructed based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood and demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons.
About: 
This article is published in Cell.The article was published on 2013-11-21 and is currently open access. It has received 810 citations till now. The article focuses on the topics: Exome.

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Neuroscience 細胞死：最近の知見

廣瀬雄一
TL;DR: In this paper, the authors describe a scenario where a group of people are attempting to find a solution to the problem of "finding the needle in a haystack" in the environment.
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Synaptic, transcriptional and chromatin genes disrupted in autism

Silvia De Rubeis, +99 more
- 13 Nov 2014 - 
TL;DR: Using exome sequencing, it is shown that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate of < 0.05, plus a set of 107 genes strongly enriched for those likely to affect risk (FDR < 0.30).
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The contribution of de novo coding mutations to autism spectrum disorder

Ivan Iossifov, +52 more
- 13 Nov 2014 - 
TL;DR: It is estimated that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation.
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Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci.

Stephen Sanders, +49 more
- 23 Sep 2015 - 
TL;DR: Analysis of de novo CNVs from the full Simons Simplex Collection replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci, including 6 CNV regions.
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Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

F. Kyle Satterstrom, +201 more
- 06 Feb 2020 - 
TL;DR: The largest exome sequencing study of autism spectrum disorder (ASD) to date, using an enhanced analytical framework to integrate de novo and case-control rare variation, identifies 102 risk genes at a false discovery rate of 0.1 or less, consistent with multiple paths to an excitatory-inhibitory imbalance underlying ASD.
References
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Journal ArticleDOI

The Sequence Alignment/Map format and SAMtools

Heng Li, +8 more
- 01 Aug 2009 - 
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, +1 more
- 01 Jul 2009 - 
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead, +3 more
- 04 Mar 2009 - 
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
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TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell, +2 more
- 01 May 2009 - 
TL;DR: The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer.
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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim, +8 more
- 25 Apr 2013 - 
TL;DR: TopHat2 is described, which incorporates many significant enhancements to TopHat, and combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes.
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The contribution of de novo coding mutations to autism spectrum disorder

Ivan Iossifov, +52 more
- 13 Nov 2014 - 

Synaptic, transcriptional and chromatin genes disrupted in autism

Silvia De Rubeis, +99 more
- 13 Nov 2014 - 

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

Stephen Sanders, +29 more
- 10 May 2012 - 

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

Brian J. O'Roak, +24 more
- 10 May 2012 - 

Spatio-temporal transcriptome of the human brain

Hyo Jung Kang, +29 more
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