User:Jarle Pahr/Genomics

Notes on personal genomics:

De novo mutations occur at <100 per generation: http://massgenomics.org/2012/08/de-novo-mutations-and-human-disease.html

The NA12878 genome from "Utah pedigree 1463" may be the genome that has been sequenced the most times. (http://blog.goldenhelix.com/?p=1725). It is a candidate for use as a reference genome with respect to sequencing quality. (http://nxseq.bitesizebio.com/articles/which-way-forward-in-ultra-high-throughput-genomic-sequencing-reference-materials-and-performance-measurements/)

NA12878 datasets: https://docs.google.com/spreadsheet/ccc?key=0ArAo1qqJJDHQdHo0U1FzQV9JYVZhdnh2TGtlb1NQZXc#gid=0

Single Nucleotide Polymorphisms (SNPs)

http://www.isogg.org/wiki/Single-nucleotide_polymorphism

Promethease: http://snpedia.com/index.php/Promethease

The number of SNPs in the human genome has been estimated to ~ 10 million (source?).

dbSNP:

http://www.ncbi.nlm.nih.gov/snp

http://www.ncbi.nlm.nih.gov/projects/SNP/

http://en.wikipedia.org/wiki/DbSNP

SNPedia:

http://www.snpedia.com/index.php/SNPedia

From SNPedia: "SNPedia is a wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. "

The current state of dbSNP: http://massgenomics.org/2012/01/the-current-state-of-dbsnp.html

Imputation

http://www.genomesunzipped.org/2013/03/learning-more-from-your-23andme-results-with-imputation.php#more-5390

http://www.ncbi.nlm.nih.gov/pubmed/20517342

Genomics projects

1000 Genomes Project

http://en.wikipedia.org/wiki/The_1000_Genomes_Project

The 1000 genomes project aims to sequence ~2500 samples at 4x to uncover most genetic variants having a frequency of at least 1 % in the populations studied.

An integrated map of genetic variation from 1,092 human genomes

[Personal Genome Project (PGP)

The Personal Genome Project aims to publish the genomes and medical records of 100 000 volunteers. As of March 2013, the number of enrolled participants is about 2500, of which there are available full-genome datasets for about 75. Some participants for which full genome datasets are not available, have uploaded data from genotyping services such as 23AndMe.

http://www.personalgenomes.org/

http://en.wikipedia.org/wiki/Personal_Genome_Project

See also:

http://arep.med.harvard.edu/PGP/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681452/

http://www.necessaryfilms.com/genome.html

http://www.personalgenomes.org/exam/v20120430-study-guide.pdf

http://blog.personalgenomes.org/

Unofficial wiki: http://wiki.personal-genome.org/index.php?title=Main_Page

http://www.ncbi.nlm.nih.gov/pubmed/22797899

International HapMap Project

Single Nucleotide Polymorphisms (SNPs) are often inherited together. The genotypes at some SNPs may thus be predicted by the genotype at one or more other SNPs. Groups of co-inherited SNPs are called "haplotypes". The HapMap project identifies common haplotypes and "tag" SNPs that uniquely identifies haplotypes.

From http://hapmap.ncbi.nlm.nih.gov/whatishapmap.html : "The number of tag SNPs that contain most of the information about the patterns of genetic variation is estimated to be about 300,000 to 600,000, which is far fewer than the 10 million common SNPs."

As part of the HapMap project, new SNPs sites were identified in order to serve as haplotype tags.

A second generation human haplotype map of over 3.1 million SNPs

Colloborative Oncology Gene-Environment Study

http://www.cogseu.org/

Online Mendelian Inheritance in Man (OMIM)

http://www.omim.org/

Blogs

SNPedia blog: http://snpedia.blogspot.no/

http://www.genomesunzipped.org/

http://massgenomics.org

http://thepersonalgenome.com/

Public genomes

http://www.snpedia.com/index.php/Genomes

https://my.personalgenomes.org/users/

George Church

Craig Venter:

http://huref.jcvi.org/

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050254

James Watson: http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/

Complete Genomics 69 Genomes dataset: http://www.completegenomics.com/public-data/69-Genomes/

Genomes unzipped: http://www.genomesunzipped.org/data

DTC genomics companies

https://www.23andme.com/

Bibliography

SNPedia: a wiki supporting personal genome annotation, interpretation and analysis: nar.oxfordjournals.org/content/40/D1/D1308.long

http://www.ncbi.nlm.nih.gov/pubmed/18154681?dopt=Abstract

Se also:

dbSNP database: http://www.ncbi.nlm.nih.gov/projects/SNP/

http://en.wikipedia.org/wiki/Full_Genome_Sequencing

http://en.wikipedia.org/wiki/Personal_genomics

http://nar.oxfordjournals.org/content/40/W1/W76.abstract

http://www.interpretome.com/

Book - Exploring personal genomics: http://exploringpersonalgenomics.org/

UCSC Genome Browser: http://genome.ucsc.edu/

CEPH panel: http://hg.wustl.edu/hdk_lab_manual/14/14_1.html

http://www.ncbi.nlm.nih.gov/pubmed/22274586

http://www.dnasnips.com/dnaSnips/Home.html