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

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. "

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

Genomics projects:

1000 Genomes Project: http://www.1000genomes.org

Personal Genome Project (PGP): http://www.personalgenomes.org/

International HapMap Project: http://hapmap.ncbi.nlm.nih.gov/

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."

Blogs:

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

http://www.genomesunzipped.org/

http://massgenomics.org

Public genomes:

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

DTC genomics companies:

https://www.23andme.com/

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

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