User:Jarle Pahr/Genomics

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Revision as of 03:04, 28 March 2013 by Jarle Pahr (talk | contribs) (Personal Genome Project (PGP))
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Notes on personal genomics:

De novo mutations occur at <100 per generation:

The NA12878 genome from "Utah pedigree 1463" may be the genome that has been sequenced the most times. ( It is a candidate for use as a reference genome with respect to sequencing quality. (

NA12878 datasets:

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:


Genomics projects

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)

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 : "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

Online Mendelian Inheritance in Man (OMIM)


SNPedia blog:

Public genomes

DTC genomics companies


SNPedia: a wiki supporting personal genome annotation, interpretation and analysis:

Se also:

dbSNP database:

Book - Exploring personal genomics:

UCSC Genome Browser: