User:Jarle Pahr/Genomics: Difference between revisions
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http://www.biomedpharmajournal.org/dnload/A-Direkvand-Moghadam--A-Delpisheh-M-Rezaeian-and-A-Khosravi4/BPJV06I02P161-167.pdf | |||
=Compression and storage= | =Compression and storage= |
Latest revision as of 09:18, 24 February 2014
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 fhas 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
Personal genomics topics
Birth and maternal health
Ruth Landau, MD. Genetic Contributions to Labor Pain and Progress. Clinics in Perinatology Volume 40, Issue 3, September 2013, Pages 575–587.
http://www.sciencedirect.com/science/article/pii/S000293780600740X
http://www.sciencedirect.com/science/article/pii/S0002937811003838
Compression and storage
Efficient storage of high throughput sequencing data using reference-based compression http://genome.cshlp.org/content/early/2011/01/18/gr.114819.110
CRAM toolkit: http://www.ebi.ac.uk/ena/about/cram_toolkit
http://genomeinformatician.blogspot.no/2012/05/dna-compression-reprise.html
The Human Genome Contracts Again: http://bioinformatics.oxfordjournals.org/content/early/2013/06/22/bioinformatics.btt362.short?rss=1
Single Nucleotide Polymorphisms (SNPs)
http://www.isogg.org/wiki/Single-nucleotide_polymorphism
SISRS: SNP Identification from Short Read Sequences: http://arxiv.org/abs/1305.3665
General Information about dbSNP, Single Nucleotide Polymorphisims, and Genetics: http://www.ncbi.nlm.nih.gov/books/NBK3856/
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
OpenSNP:
SNPnexus:
dbGaP:
http://www.ncbi.nlm.nih.gov/gap
GWAScentral:
Human Gene Mutation Databasse:
NextBio:
http://www.nextbio.com/b/nextbioCorp.nb
http://www.hgmd.cf.ac.uk/ac/index.php
Online Mendelian Inheritance in Man (OMIM): http://www.ncbi.nlm.nih.gov/omim
Interesting SNPs
- Polymorphism in LRRK2. Associated with Parkinson's disease.
- My genotype:GG (normal)
- Silent mutation in the oxytocin receptor (OXTR) gene.
- My genotype: AG (reference GG)
- My genotype: AA (reference: TT)
- SNP determining eye color?
- My genotype: GG (minor allele: G)
- My genotype: AA (normal)
- "Warrior vs Worrier"
- My genotype: GG ("warrior")
Imputation
Genotype imputation for genome-wide association studies.: http://www.ncbi.nlm.nih.gov/pubmed/20517342
IMPUTE 2: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html
See also http://home.uchicago.edu/~bhowie/software.html
expressed quantitative trait loci (eQTL)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650863/
Companies
http://www.bionanogenomics.com/
Genomics projects
The NHGRI Genome Sequencing Program (GSP): http://www.genome.gov/10001691
100k foodborne pathogen genome project
http://100kgenome.vetmed.ucdavis.edu/
Human Genome Diversity Project
http://en.wikipedia.org/wiki/Human_Genome_Diversity_Project
Genome 10K Project
Aims to obtain genomic information for 10 000 vertebrate species.
http://genome10k.soe.ucsc.edu/
Cancer Genome Atlas
https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp
Human Microbiome Project
http://commonfund.nih.gov/hmp/
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001377
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
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."
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
ENCODE
Colloborative Oncology Gene-Environment Study
Online Mendelian Inheritance in Man (OMIM)
Direct to Consumer (DTC) genotypcing services
23andme:
Interpretation tools
OpenSNP: http://opensnp.org/
Interpretome: http://esquilax.stanford.edu/
See http://www.ncbi.nlm.nih.gov/pubmed/22174289
http://nar.oxfordjournals.org/content/early/2013/04/29/nar.gkt342.full
http://www.ensembl.org/index.html
Journals
Genome Biology: http://genomebiology.com/
Blogs and commentary
http://genomeinformatician.blogspot.no
http://www.thegenesherpa.blogspot.no/
SNPedia blog: http://snpedia.blogspot.no/
http://www.genomesunzipped.org/
http://omicsomics.blogspot.no/
http://core-genomics.blogspot.ca/
http://thegenomefactory.blogspot.no/
UW Genome Sciences - Distinguished Faculty Interview Series: Joe Felsenstein : https://www.youtube.com/watch?v=3wO39cm0a2M
1000$ Genome / economy of sequencing
http://www.bio-itworld.com/2010/09/28/1Kgenome.html
Software
myPEG: http://mypeg.info/
Genomic hyperbrowser: http://hyperbrowser.uio.no/hb/
http://www.dnasearchengine.com/
ANNOVAR: http://www.openbioinformatics.org/annovar/
http://www.ncbi.nlm.nih.gov/tools/gbench/
Genome Workbench SNP Tools (GST) Quick Start: http://www.ncbi.nlm.nih.gov/books/NBK3859/
Variant annotation tools: http://varianttools.sourceforge.net/Annotation/DbSNP
A review of genomic data warehousing systems: http://bib.oxfordjournals.org/content/early/2013/05/14/bib.bbt031.short?rss=1&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer&utm_content=buffer656ea
MISO open-source LIMS: http://www.tgac.ac.uk/miso/
Galaxy: https://main.g2.bx.psu.edu/
Enlis: http://www.enlis.com/research_edition.html
Public genomes
http://www.snpedia.com/index.php/Genomes
https://my.personalgenomes.org/users/
Craig Venter:
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
Banana genome hub: http://banana-genome.cirad.fr/
Crowdsourcing the Corpasome: http://www.youtube.com/watch?v=sV7dD1DcQwQ&feature=youtu.be&a
DTC genomics companies
Ethical, Legal and Social Implications (ELSI)
http://www.genome.gov/10001618
http://www.genomicslawreport.com/
http://www.technologyreview.com/featuredstory/513691/prenatal-dna-sequencing/
Genomic privacy:
http://www.nature.com/news/privacy-protections-the-genome-hacker-1.12940
Databases
See also: NCBIs interactions with Locus-Specific Data Bases (LSDB): http://www.ncbi.nlm.nih.gov/refseq/rsg/lsdb/
ALFRED The ALlele FREquency Database: http://alfred.med.yale.edu/
PheGenI - Phenotype Genotype Integrator: http://www.ncbi.nlm.nih.gov/gap/phegeni
http://www.rostlab.org/services/snpdbe/dosearch.php?id=mutation&val=
The Human Gene Mutation Database (HGMD): http://www.hgmd.cf.ac.uk/ac/index.php
dbSNP
http://en.wikipedia.org/wiki/DbSNP
Information: General Information about dbSNP as a Database Resource: http://www.ncbi.nlm.nih.gov/books/NBK44469/
dbSNP fact sheet: ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_SNP.pdf
Finding Information in a dbSNP Data Report: http://www.ncbi.nlm.nih.gov/books/NBK44476/
SNP faq archive: http://www.ncbi.nlm.nih.gov/books/NBK3848/
NCBI Handbook chapter 5 - the dbSNP database: http://www.ncbi.nlm.nih.gov/books/NBK21088/
dbSNP data content information: http://www.ncbi.nlm.nih.gov/books/NBK3853/
Using dbSNP Data Reports: http://www.ncbi.nlm.nih.gov/books/NBK3854/
Clustered RefSNPs (rs) and Other Data Computed in House: http://www.ncbi.nlm.nih.gov/books/NBK44417/
SNP attributes: http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html
Searching:
General dbSNP Search Options: http://www.ncbi.nlm.nih.gov/books/NBK44371/
Searching NCbI's dbSNP database: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078622/
SNP search: http://www.ncbi.nlm.nih.gov/snp?TabCmd=Limits
Updates:
The database is updated periodically, resulting in a new build number. The current build number (april 2012) is 137. For every new build, refSNPs (rs#) are re-mapped and re-clustered on the latest genome assembly. SNP submissions (ss#) which have the same position in the genome are merged into one rs#. rs numbers which become redundant after merging are not reused. SNPs and indels are not merged, as these are distinct types of "mutational events" (http://www.ncbi.nlm.nih.gov/books/NBK21088/).
Note that from Homo Sapiens annotation release 104 and onwards, annotation releases are given separate numbers, distinct from genome build numbers.
rs and ss numbers:
All new submissions are given an ss number. After each mapping, all submissions which are mapped to the same site are clustered in one rs number. The submission (ss number) with the longest flanking sequence becomes the rs cluster exemplar. (http://www.ncbi.nlm.nih.gov/books/NBK44391/)
The alleles field:
The order of the alleles listed in the alleles field does NOT carry any biological meaning. Alleles are listed in alphabetical order. Note that some SNPs have different minor alleles between different populations. dbSNP maps SNPs to all major assemblies - the different assemblies sometimes have different alleles at a particular SNP position.
N and Y designations (www.ncbi.nlm.nih.gov/books/NBK44476/):
"N" is the designation for "tested, but results indeterminate".
"Y" is the designation for genotypes from males for SNPs that map to the X chromosomes
Sample size:
There are two sample size numbers: The assay sample size is the number of chromosomes used to ascertain or discover the variation. The population sample size is the number of chromosomes used as the denominator when computing estimates of allele frequencies.
refSNP validation and quality:
"Double hit": refSNPs with both alleles seen at least twice.
Variation functional class (http://www.ncbi.nlm.nih.gov/books/NBK21088/#ch5.ch5_4_11_1): For each SNP, a functional context is determined by inspecting the flanking sequences, describing the function of the sequence the SNP is located in. Examples are "locus region", "coding synon", "coding non-synon", mRNA-UTR, intron.
If either allele in the variation is a non-synonymous change, then the variation is classified as non-synonymous; otherwise, the variation is classified as a synonymous variation
Global minor allele frequency (MAF):
The minor allele frequency for a given rs, reported with respect to a default global population (currently based on 1000 genomes project data). Given 3 alleles with frequencies of 0.50, 0.49, and 0.01, the MAF will be reported as 0.49. "MAF source": Data source for MAF calculation.
HGVS names:
SNP name(s) according to Human Genome Variation Society nomenclature. See http://www.hgvs.org/mutnomen/recs.html#general. Note that "according to HGVS nomenclature, the allele before the ">" sign is simply the base located on the reference sequence at the position specified in the HGVS name — it does not have to be the major allele." (http://www.ncbi.nlm.nih.gov/books/NBK44476/)
Allele origin:
The origin of variant alleles reported by the submitter(s). Possible values are germline, somatic or unknown.
Ancestral allele (http://www.ncbi.nlm.nih.gov/books/NBK84687/):
Ancestral allele version, as determined by comparison with Chimpanzee DNA.
Map to genome build: Version number of the genome assembly used for SNP mapping.
Integrated maps: Shows information on the SNP location and mapping in available genome assemblies. The contig alleles on different assemblies are often the same, but not always.
FTP access:
ftp://ftp.ncbi.nlm.nih.gov/snp/00readme.txt
Citation: http://genome.cshlp.org/content/9/8/677.full
JSNP
http://snp.ims.u-tokyo.ac.jp/index.html
SNPedia
http://www.genome.gov/gwastudies/
Genome annotation and curation
Concensus Coding Sequence (CCDS) project: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi
MicroScope: http://www.genoscope.cns.fr/agc/microscope/home/index.php
Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
BaSys: http://basys.ca/
RAST: http://rast.nmpdr.org/ ' http://www.jcvi.org/cms/index.php?id=141
IGS annotation service: http://ae.igs.umaryland.edu/cgi/index.cgi
NCBI prokaryotic genome annotation pipeline: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi
AgeS: http://bhsai.org/software/
See also http://thegenomefactory.blogspot.no/2013/03/bacterial-genome-annotation-systems.html
http://www.gmod.org/wiki/WebApollo
RATT Rapid Anotation Transfer Tool: http://ratt.sourceforge.net/
Manatee: http://manatee.sourceforge.net/
Review - The automatic annotation of bacterial genomes. http://bib.oxfordjournals.org/content/14/1/1.full
A semi-automated genome annotation comparison and integration scheme: http://www.biomedcentral.com/1471-2105/14/172/abstract
Educational and instructional material
Research groups
Bibliography
Sequencing studies in human genetics: design and interpretation: http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg3455.html
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
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
Compressive genomics:
Efficient storage of high throughput sequencing data using reference-based compression: http://genome.cshlp.org/content/early/2011/01/18/gr.114819.110
Medical genomics and genomic medicine
Notable accomplishments in genomic medicince: http://www.genome.gov/27551536
http://www.perkinelmer.com/pdfs/downloads/CST_RGHS_SF_Dinwiddie.pdf
http://ww2.biol.sc.edu/~elygen/biol303/2012%20papers/Sequencing%20for%20diagnosis.pdf
SSAGA, Symptom and Sign Assisted Genome Analysis:
Report on use of medical genetics in Norway (Norwegian): http://home.hio.no/~nilss/rapport.pdf
Companies:
Prenatal sequencing:
http://www.technologyreview.com/news/510181/a-brave-new-world-of-prenatal-dna-sequencing/
www.technologyreview.com/featuredstory/513691/prenatal-dna-sequencing/
http://www.genomeweb.com/sequencing/ready-prenatal-sequencing
Microarrays and DNA Sequencing Improve Prenatal Testing: http://www.medscape.com/viewarticle/775687
Prenatal Whole Genome Sequencing: Just Because We Can, Should We? http://www.thehastingscenter.org
/Publications/HCR/Detail.aspx?id=5909
Noninvasive prenatal diagnosis empowered by high-throughput sequencing.: http://www.ncbi.nlm.nih.gov/pubmed/22467171
http://blogs.discovermagazine.com/gnxp/2012/08/yes-we-should-prenatal-sequencing/#.UYOIFMq95rl
http://www.technologyreview.com/news/510181/a-brave-new-world-of-prenatal-dna-sequencing/
Clinical Diagnosis by Whole-Genome Sequencing of a Prenatal Sample: http://www.nejm.org/doi/full/10.1056/NEJMoa1208594
In the news:
http://www.uq.edu.au/news/index.html?article=26167
Personal genomics
Do-it-yourself genetic testing: http://genomebiology.com/2010/11/10/404
http://www.portablegenomics.com/
"integrated personal omics profiling" (iPOP): http://download.cell.com/chemistry-biology/pdf/PIIS1074552113001749.pdf?intermediate=true
SeqAnswers personal genomics forum: http://seqanswers.com/forums/forumdisplay.php?f=14
Metagenomics
Software:
Metagenomic Approaches for Exploiting Uncultivated Bacteria as a Resource for Novel Biosynthetic Enzymology: http://download.cell.com/chemistry-biology/pdf/PIIS1074552113001683.pdf?intermediate=true
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota: http://www.sciencemag.org/content/335/6068/587