Tag: Ancestry

CCH 20141012 – Identify Genomic Regions of Shared Ancestry

CCH 20141012

:: DESCRIPTION

CCH (Combinatorial Conflicting Homozygosity) uses dense Single Nucleotide Polymorphism (SNP) genotypes to identify regions of the genome inherited from a common ancestor among any or all subsets of a group. Analysis is rapid and can identify loci containing genes for dominant traits. CCH is robust to the presence of phenocopies and can detect undisclosed shared common ancestry.

::DEVELOPER

CCH team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python

:: DOWNLOAD

 CCH

:: MORE INFORMATION

Citation

Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies.
Levine AP, Connor TM, Oygar DD, Neild GH, Segal AW, Maxwell PH, Gale DP.
BMC Genomics. 2015 Mar 10;16:163. doi: 10.1186/s12864-015-1360-4.

LAMP 2.5 / LAMP-LD 1.1 – Estimate Locus Specific Ancestry

LAMP 2.5 / LAMP-LD 1.1

:: DESCRIPTION

LAMP (Local Ancestry in adMixed Populations) is a software for the inference of locus-specific ancestry in recently admixed populations. LAMP computes the ancestry structure for overlapping windows of contiguous SNPs and combines the results with a majority vote.

LAMP-LD is a software package for the inference of locus-specific ancestry in recently admixed populations.

::DEVELOPER

Computational Genetics Group

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LAMP / LAMP-LD

:: MORE INFORMATION

Citation:

Sriram Sankararaman, Srinath Sridhar, Gad Kimmel and Eran Halperin,
Estimating Local Ancestry in Admixed Populations,
The American Journal of Human Genetics, Volume 82, Issue 2, 290-303, 2008.

Bioinformatics. 2012 May 15;28(10):1359-67. doi: 10.1093/bioinformatics/bts144. Epub 2012 Apr 11.
Fast and accurate inference of local ancestry in Latino populations.
Baran Y, Pasaniuc B, Sankararaman S, Torgerson DG, Gignoux C, Eng C, Rodriguez-Cintron W, Chapela R, Ford JG, Avila PC, Rodriguez-Santana J, Burchard EG, Halperin E.

FastPop – Infer Intercontinental Ancestry using Genetic data

FastPop

:: DESCRIPTION

FastPop is an efficient R package that fills the gap between Structure and Eigenstrat. It can: 1, generate PCA scores that identify ancestral origins and can be used for multiple studies; 2, infer ancestry information for data arising from two or more intercontinental origins.

::DEVELOPER

FastPop team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 FastPop

:: MORE INFORMATION

Citation

FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data.
Li Y, Byun J, Cai G, Xiao X, Han Y, Cornelis O, Dinulos JE, Dennis J, Easton D, Gorlov I, Seldin MF, Amos CI.
BMC Bioinformatics. 2016 Mar 9;17(1):122. doi: 10.1186/s12859-016-0965-1.

SABER + 12_14 – Inferring Locus-specific Ancestry in Admixed Individuals

SABER + 12_14

:: DESCRIPTION

SABER+ implements a Markov-Hidden Markov Model for inferring locus-specific ancestry in admixed individuals

:: DEVELOPER

Tang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

 SABER

:: MORE INFORMATION

Citation

Am J Hum Genet. 2006 Jul;79(1):1-12. Epub 2006 May 17.
Reconstructing genetic ancestry blocks in admixed individuals.
Tang H1, Coram M, Wang P, Zhu X, Risch N.

PCAdmix 1.0 – Local Ancestry Deconvolution

PCAdmix 1.0

:: DESCRIPTION

PCAdmix is a method that estimates local ancestry via principal components analysis (PCA) using phased haplotypes.  The method considers data chromosome by chromosome.

:: DEVELOPER

the Bustamante Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

  PCAdmix

:: MORE INFORMATION

Citation

Hum Biol. 2012 Aug;84(4):343-64. doi: 10.3378/027.084.0401.
PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations.
Brisbin A1, Bryc K, Byrnes J, Zakharia F, Omberg L, Degenhardt J, Reynolds A, Ostrer H, Mezey JG, Bustamante CD.

HRRA – Homozygous Regions of Recent Ancestry

HRRA

:: DESCRIPTION

HRRA can be used with recessive Mendelian diseases when only one or a few patients are available and with no genealogy data.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HRRA

:: MORE INFORMATION

Citation

Hum Mutat. 2011 Mar;32(3):345-53. doi: 10.1002/humu.21432.
Homozygosity mapping on a single patient: identification of homozygous regions of recent common ancestry by using population data.
Zhang L1, Yang W, Ying D, Cherny SS, Hildebrandt F, Sham PC, Lau YL.

LASER 2.04 – Locating Ancestry using SEquencing Reads

LASER 2.04

:: DESCRIPTION

LASER is a C++ software package that can estimate individual ancestry directly from genome-wide shortgun sequencing reads without calling genotypes.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 LASER

:: MORE INFORMATION

Citation

Nat Genet. 2014 Apr;46(4):409-15. doi: 10.1038/ng.2924. Epub 2014 Mar 16.
Ancestry estimation and control of population stratification for sequence-based association studies.
Wang C et cl.

hindex 1.42 – Calculates a Hybrid Index for Individuals of unknown Ancestry

hindex 1.42

:: DESCRIPTION

hindex calculates a hybrid index for individuals of unknown ancestry. The index is based on information from molecular markers and uses maximum-likelihood to estimate the proportion of alleles that were inherited from one of two hybridizing parental species.

::DEVELOPER

Buerkle lab ,University of Wyoming

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 hindex

:: MORE INFORMATION

Citation:

Buerkle, C. Alex. 2005.
Maximum-likelihood estimation of a hybrid index based on molecular markers.
Molecular Ecology Notes 5: 684-687

HAPMIX v2 – Identify Ancestry Segment

HAPMIX v2

:: DESCRIPTION

HAPMIX is an application for accurately inferring chromosomal segments of distinct ancestry in admixed populations, using dense genetic data.

::DEVELOPER

Simon Myers

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HAPMIX

:: MORE INFORMATION

Citation:

Price et al.,
Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations
PLoS Genet (2009).

ANCESTRYMAP 2.0 – Find Skews in Ancestry

ANCESTRYMAP 2.0

:: DESCRIPTION

ANCESTRYMAP finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. Admixture mapping is a method for localizing disease causing genetic variants that differ in frequency across populations. It is most advantageous to apply this approach to populations that have descended from a recent mix of two ancestral groups that have been geographically isolated for many tens of thousands of years: for example, African Americans have both West African and European American ancestry. The approach assumes that near a disease causing gene there will be enhanced ancestry from the population that has greater risk of getting the disease. Thus if one can calculate the ancestry along the genome for an admixed sample set, one could use that to identify disease causing gene variants. The figure below shows a schematic of how a disease locus would appear in an admixture scan of patients and controls.

::DEVELOPER

Reich laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Unix

:: DOWNLOAD

ANCESTRYMAP for Linux ; for Unix

:: MORE INFORMATION

Citation:

Patterson et al. 2004
Methods for High-Density Admixture Mapping of Disease Genes
Am. J. Hum. Genet. 74:000–000, 2004