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Revision as of 07:09, 28 March 2013
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/)
Single Nucleotide Polymorphisms (SNPs)
The number of SNPs in the human genome has been estimated to ~ 10 million (source?).
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
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.
[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.
Unofficial wiki: http://wiki.personal-genome.org/index.php?title=Main_Page
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.
Colloborative Oncology Gene-Environment Study
Online Mendelian Inheritance in Man (OMIM)
SNPedia blog: http://snpedia.blogspot.no/
Complete Genomics 69 Genomes dataset: http://www.completegenomics.com/public-data/69-Genomes/
Genomes unzipped: http://www.genomesunzipped.org/data
DTC genomics companies
SNPedia: a wiki supporting personal genome annotation, interpretation and analysis: nar.oxfordjournals.org/content/40/D1/D1308.long
dbSNP database: http://www.ncbi.nlm.nih.gov/projects/SNP/
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