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MacArthur Lab | Extracting useful information from large genomic datasets.

The MacArthur lab uses cutting-edge genomic technologies at massive scale to understand the impact of human genetic variation, and to provide answers to families affected by rare genetic diseases. exome aggregation We lead an international consortium that has assembled ExAC, the world's largest single collection of sequencing data from human protein-coding gene regions (the exome),…

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MacArthur Lab | Extracting useful information from large genomic datasets. | macarthurlab.org Reviews

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The MacArthur lab uses cutting-edge genomic technologies at massive scale to understand the impact of human genetic variation, and to provide answers to families affected by rare genetic diseases. exome aggregation We lead an international consortium that has assembled ExAC, the world's largest single collection of sequencing data from human protein-coding gene regions (the exome),…

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MacArthur Lab | Extracting useful information from large genomic datasets. | macarthurlab.org Reviews

https://macarthurlab.org

The MacArthur lab uses cutting-edge genomic technologies at massive scale to understand the impact of human genetic variation, and to provide answers to families affected by rare genetic diseases. exome aggregation We lead an international consortium that has assembled ExAC, the world's largest single collection of sequencing data from human protein-coding gene regions (the exome),…

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macarthurlab.org

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Code | MacArthur Lab

https://macarthurlab.org/code

Extracting useful information from large genomic datasets. We believe in making our code open source. The following GitHub repositories contain genomics tools you may find useful:. Is a software tool we use for searching for causal variants in Mendelian disease families. Is a plugin for the Ensembl Variant Effect Predictor that improves the detection and filtering of candidate protein-truncating variants. Is the code behind our ExAC browser. Provides tools to parse NCBI’s ClinVar. Enter your comment here.

2

Rare disease gene discovery | MacArthur Lab

https://macarthurlab.org/rare-disease

Extracting useful information from large genomic datasets. Rare disease gene discovery. Rare disease gene discovery. We develop and apply genomic approaches (especially exome, whole-genome and transcriptome sequencing) and informatic methods to discover disease-causing mutations in severe disease patients, with a particular focus on neuromuscular diseases such as muscular dystrophy. Our tool seqr. Is an intuitive browser-based system for analyzing exome and genome data from rare disease families. Convert...

3

What do we miss with exome sequencing? | MacArthur Lab

https://macarthurlab.org/2014/07/21/what-do-we-miss-with-exome-sequencing

Extracting useful information from large genomic datasets. What do we miss with exome sequencing? The exome era turns five years old this fall, with the anniversary of the “Targeted capture and massively parallel sequencing of 12 human exomes” [ Ng 2009. Born at a time when whole genome sequencing cost. WGS has remained a last resort for a few reasons: it’s still a bit more expensive than WES, it produces more data we have to process and store, and despite some notable recent advances [ Ritchie 2014.

4

Using gene expression data to interpret variation | MacArthur Lab

https://macarthurlab.org/gene-expression

Extracting useful information from large genomic datasets. Using gene expression data to interpret variation. Using gene expression data for variant interpretation. We use transcriptome sequencing (RNA-seq) approaches to better characterize the impact of DNA sequence variants on human gene function. As part of the GTEx Project. Announcing the Exome Aggregation Consortium paper. Reproduce all the figures! A user’s guide to ExAC, part 2. A personal journey to quantify disease risk. Blog at WordPress.com.

5

Loss of function variants | MacArthur Lab

https://macarthurlab.org/lof

Extracting useful information from large genomic datasets. Loss of function variants. Our work on investigating LoF variants in human genes – which we’re calling the Human Knockout Project – was recently highlighted in. This was a very large collaborative project involving researchers at the Sanger Institute, Yale University, and a number of other institutions, and used data made available by the 1000 Genomes Project. A pre-formatted version of the manuscript is available here. Media and online coverage.

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genomesunzipped.org

fdr « Genomes Unzipped

http://genomesunzipped.org/tag/fdr

Tag Archive for 'fdr'. Incorporating false discovery rates into genetic association in autism. Written by Guest Author. This guest post was contributed by Joseph Buxbaum, Mark Daly, Silvia De Rubeis, Bernie Devlin, Kathryn Roeder, and Kaitlin Samocha from the Autism Sequencing Consortium (see affiliations and details at the end of the post). In a paper published in. Continue reading ‘Incorporating false discovery rates into genetic association in autism’. Eight types of schizophrenia? Not so fast…. On In...

genomesunzipped.org

Guest Posts « Genomes Unzipped

http://genomesunzipped.org/category/guest-posts

Archive for the 'Guest Posts' Category. Incorporating false discovery rates into genetic association in autism. Written by Guest Author. This guest post was contributed by Joseph Buxbaum, Mark Daly, Silvia De Rubeis, Bernie Devlin, Kathryn Roeder, and Kaitlin Samocha from the Autism Sequencing Consortium (see affiliations and details at the end of the post). In a paper published in. Continue reading ‘Incorporating false discovery rates into genetic association in autism’. Eight types of schizophrenia?

genomesunzipped.org

Data/Code « Genomes Unzipped

http://genomesunzipped.org/data

Genomes Unzipped is a collaborative online project. Aiming to provide genetic testing customers with the knowledge and tools they need to make the most of their own genetic data. As part of the project our members. Are taking commercial genetic tests and making the raw data publicly available for others to download, analyse and reuse. There are currently three ways for users to access our genotype data. 1: Our Genome Browser. Download genotype data for a particular SNP by clicking on it. 3: Use Our API.

genomesunzipped.org

Resources « Genomes Unzipped

http://genomesunzipped.org/resources

This list of resources is still under construction. If you have suggestions for useful resources not on the list, email us. Test your knowledge of genomics by taking the test given to all Personal Genome Project participants. PgEd (Personal Genetics Education Project). Teaching resources on personal genetics. Background material on genomics, produced by the Wellcome Trust Sanger Institute. Talking Glossary of Genetic Terms. A Wellcome Trust-funded resource on understanding genetics and genomics. Genomes ...

genomesunzipped.org

Incorporating false discovery rates into genetic association in autism « Genomes Unzipped

http://genomesunzipped.org/2014/11/incorporating-false-discovery-rates-into-genetic-association-in-autism.php

Eight types of schizophrenia? Not so fast…. Incorporating false discovery rates into genetic association in autism. Written by Guest Author. This guest post was contributed by Joseph Buxbaum, Mark Daly, Silvia De Rubeis, Bernie Devlin, Kathryn Roeder, and Kaitlin Samocha from the Autism Sequencing Consortium (see affiliations and details at the end of the post). In a paper published in. Why is the FDR a good fit to our study design? Specifically considering only de novo LoF mutations observed in the 2297...

genomesunzipped.org

Making sequencing simpler with nanopores « Genomes Unzipped

http://genomesunzipped.org/2012/02/making-sequencing-simpler-with-nanopores.php

All genomes are dysfunctional: broken genes in healthy individuals. Identifying targets of natural selection in human and dog evolution ». Making sequencing simpler with nanopores. Written by Luke Jostins. The Advances in Genome Biology and Technology. Oxford Nanopore, who we have written about before. Today announced two new sequencing machines. To come out this year. The announcement has caused quite a buzz amoungst, well, everyone. Nature. All have reported on it, and bloggers Nick Loman. The cost is ...

genomesunzipped.org

risk prediction « Genomes Unzipped

http://genomesunzipped.org/tag/risk-prediction

Tag Archive for 'risk prediction'. Eight types of schizophrenia? Not so fast…. Written by Guest Author. Editor’s note: this guest post was contributed by ten leading psychiatric geneticists (see author list at the end of the post) in response to the headline-grabbing claims of a recent paper claiming to have identified eight genetic sub-types of schizophrenia. Similar text has also been posted on PubMed Commons. And elsewhere. [DM]. In a study published on September 15, Arnedo. Not so fast…’. Claiming to...

genomesunzipped.org

schizophrenia « Genomes Unzipped

http://genomesunzipped.org/tag/schizophrenia

Tag Archive for 'schizophrenia'. Eight types of schizophrenia? Not so fast…. Written by Guest Author. Editor’s note: this guest post was contributed by ten leading psychiatric geneticists (see author list at the end of the post) in response to the headline-grabbing claims of a recent paper claiming to have identified eight genetic sub-types of schizophrenia. Similar text has also been posted on PubMed Commons. And elsewhere. [DM]. In a study published on September 15, Arnedo. Not so fast…’. Study The Hom...

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MacArthur Lab | Extracting useful information from large genomic datasets.

Extracting useful information from large genomic datasets. The MacArthur lab uses cutting-edge genomic technologies at massive scale to understand the impact of human genetic variation, and to provide answers to families affected by rare genetic diseases. We lead an international consortium that has assembled ExAC. Rare disease gene discovery. Is an intuitive online portal for exploring exome and whole-genome sequencing data from rare disease families. Read more. Loss-of-function (LoF) variants – g...

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