The analysis of y chromosome haplotypes can thus provide additional information for inferring the origins and genetic relationships of iberian cattle. Haplotypes and haplogroups were analyzed and compared between different ethnic groups. Ychromosome haplotype analysis in antioquia colombia. Put simply, haplotype is a closelyknit group of genes which a child inherits from one parent. By analysis of the genetic structure of the y chromosome, the paternal ancestry of the. Haplotype may refer to only one locus or to an entire genome. Genotype data from 12000 holstein bulls will be analyzed and a haplotype database will be created. Haplotype analysis of the polymorphic 17 ystr markers in kerala. Author summary ychromosome dna profiles are important in forensic science.
About nevgen predictor, and brief description how it works in english autosomal pca charts of europe, near east and mediterranean. On the pc, it is compatible with excel 97 upwards under windows 95, 98 and 2000, while it has been extensively tested and run in excel 2002 and excel 2003 under windows xp. The key idea missing from current approaches is that y profile matches are due to patrilineal. Conceptual differences between ibd analysis and local ancestry inference. Jun 23, 2015 a total of 675 distinct haplotypes were observed, of which 649 were unique. The y chromosome is not necessary for the male phenotype. The y chromosome haplotype reference database yhrd is an open access, annotated collection of population samples typed for y chromosomal sequence variants. Y chromosome and mtdna geographic haplogroup assignation. In a few rare cases, the sry gene has been translocated moved to the x chromosome by accident. Aug 21, 2012 the evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time.
The y chromosome haplotype reference database yhrd is a computing platform, which allows acquisition, distribution, evaluation and interpretation of forensic dna datasets. Free online y chromosome haplotype reference database for use in forensic casework. Because y str haplotype frequencies are required to provide statistical estimates of the significance of a match between forensic samples, local databases must be developed taking the demographic history of the investigated population into account. Author summary y chromosome dna profiles are important in forensic science, particularly when a male has been accused of assaulting a female. Integrating ychromosome, mitochondrial, and autosomal data. Snps and haplotype inference 10810, cmb lecture 10 eric xing polymorphism. Haplotype simple english wikipedia, the free encyclopedia.
However, as i know, there is no available tool to predict y haplogroup when you provide vcf file containing snps information as input. Haplogroup short form, with the name of a snp observed in the derived state. Excavating y chromosome haplotype strata in anatolia. Haplotypes of the four population groups were compared using the arlequin software, version 3. The major components haplogroups e3b, g, j, i, l, n, k2, and r1. Y chromosome haplotype analysis in purebred dogs semantic. Haplotype phase inference software tools population. Fugue em based haplotype estimation and association tests in unrelated and nuclear families. Suppose suspect and crime stain have the same y chromosome haplotype. For effective analysis and interpretation of y chromosome ngs data, we present yleaf, a publically available, automated, userfriendly software for highresolution y chromosome haplogroup inference independently of library and sequencing methods. Accordingly, the haplotype analysis of y chromosome has attracted much attention in the past 10 years567 8 9. Haplogroup was defined according to ycc nomenclature 16,17.
A haplotype can describe a pair of genes inherited together from one parent on one chromosome, or it can describe all of the genes on a chromosome that were inherited together from a single parent. Given the genotypes of a sample of individuals from a population, haplotype phasing attempts to infer the haplotypes of the sample using haplotype. Haplotype analysis from bovine genotype data george mason. The results will have immediate impact on other research groups and stakeholders waiting to use haplotype information. Genetic population structure will be analyzed and regions of positive selection will be identified. All analyses were performed using r statistical software v2. Im looking for a command line based tool that can be used to infer the ancestral haplotype from y chromosome variants.
A haplotype greek haploos simple is a combination of alleles at multiple linked loci that are transmitted together. Population genetic analysis of 36 ychromosomal strs yields. Y leaf a tool for performing haplogroup predictions from next generation sequencing data bam or fastq files. Outline 1 haplotype based disease association studies genetic markers lungcancer example the haplologitcommand new capabilities 2 genomewide association studies gwas sliding windows gwas of lungcancer data 3 future work yulia marchenko statacorp haplotype analysis of casecontrol data september 9, 2010 2 41. Our results indicate that the o3m122 lineage is dominant in east asian populations, with an average frequency of 44. Haploblock is a software program which provides an integrated approach to haplotype block identification, haplotyping snps or haplotype phasing, resolution or reconstruction and linkage disequilibrium ld mapping or genetic association studies. Softgenetics software powertools for genetic analysis. Ychromosome polymorphisms and ethnic group a combined str. Is there any free software to make a haplotype network or a haplotype spanning network from. If, for a given sample, yhaplo observes no derived alleles at isogg snps on the upper branches of the y chromosome phylogeny, it will call the sample haplogroup a, since all human y chromosome lineages are technically sublineages of a. A haplotype is a collection of specific alleles particular dna sequences in a cluster of tightlylinked genes on a chromosome that are likely to be inherited together.
Audio analysis resynthesis the way darwin would have done it if he were only into computer music. Phylogenetic trees of ychromosomal haplogroups eupedia. A haplotype is a collection of specific alleles particular dna sequences in a cluster of tightlylinked genes on a chromosome. Haplotype analysis of the polymorphic 17 ystr markers in kerala nontribal populations. We propose an algorithm for counting similarity between str haplotypes. We have genotyped the g1defining marker m285 in 27 eurasian populations n 5,346, analyzed 367 m285positive samples using 17 y strs, and sequenced 11 mb of the y chromosome in 20 of these samples to an. Sequences were analyzed using the seqman ii software v6. Therefore, the y chromosome haplogroup composition of a sample from alagoas population was determined, through the analysis of 24 y snps.
Plink genetic toolset haplogroup em215 y dna software. Predicted haplogroups in the slovak haban population. Software for human y chromosomal haplogroup inference from nextgeneration sequencing data. However, the analysis of y chromosome genetic diversity shows that hy3, an sscy haplotype completely absent from international breeds, has an average frequency of 0. A total of 17 y specific str loci were studied in 12 districts of the european part of russia aiming to ascertain the amount of substructure required for the construction of a representative regional database. The word haplotype is derived from the word haploid, which describes cells with only one. Pdf y chromosome haplotype analysis in purebred dogs. Jan 29, 2008 y chromosome short tandem repeat str haplotypes show a substantial interpopulation differentiation both on a worldwide and continental scale 1, 2. The trees on this page represents the phylogeny of european and middle eastern y chromosomal dna y dna haplogroups. Polymorphic markers on the malespecific part of the y chromosome. Cinnioglu 2004 excavating ychromosome haplotype strata in.
Phylogeographic analysis of haplogroup e3bem215 y chromosomes reveals multiple migratory events within and out of africa 032004. Because the y chromosome is transmitted from fathers to sons only, strsnp polymorphism. The haplomatch program for comparing ychromosome str. To our knowledge, extended y chromosome haplotypes that combine information from strs and snps have not been used to study genetic relationships among cattle breeds. Y str analysis focuses on short tandem repeats strs found on the y chromosome, only carried by male individuals. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. According to snps haplogroups which are the age of the first extinction event tend to be around 4550 kya. This finding gives strong support to the hypothesis of a direct far eastern introduction in africa. A y dna haplogroup is a group of men sharing the same series of mutations on their y chromosome, which they inherited from a long line of common paternal ancestors. A haplotype is a group of genes within an organism that was inherited together from a single parent. Mar 26, 2014 y chromosome genotyping of biallelic markers. Y chromosome haplotype analysis in purebred dogs request pdf.
Softgenetics, software powertools that are changing the genetic analysis softgenetics software powertools for genetic analysis softgenetics software powertools for genetic analysis provides current uptodate information and pricing on all products. Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. A total of 1214 y chromosomes, positive for e haplogroups, were considered in the analysis. Increased resolution of y chromosome haplogroup t defines relationships among populations of the near east, europe, and africa 112012. Software for human ychromosomal haplogroup inference from nextgeneration sequencing data. A study of a software tool, haplogroup classifier, developed at the university of arizona showed that by using machine learning algorithms and data derived from a set of y linked strs, it was possible to assign y chromosome haplogroups to individual samples with a high degree of accuracy schlecht et al.
The sry gene is required, however, and it is almost always located on the y chromosome. Strs analysis found 299 different haplotypes and snps analysis 11 different haplogroups. Ychromosomal aaron is the name given to the hypothesized most recent common ancestor of the patrilineal jewish priestly caste known as kohanim. Jan 22, 2020 genotyping arrays with few y chromosome probes. The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. A haplotype haploid genotype is a group of alleles in an organism that are inherited together. Haplotype analysis software for analysis of haplotype data. Here, we present a systematic sampling and genetic screening of an east asianspecific ychromosome haplogroup o3m122 in 2,332 individuals from diverse east asian populations. In the case of diploid organisms such as humans, a genomewide haplotype comprises one member of the pair of alleles for each locus that is, half of a diploid genome. The loci lie in the nonrecombining part of the y chromosome, which behaves like a single locus and so the y profile can be regarded as a single allele, or haplotype.
The complexity of both, y tree and ngs data provide challenges for haplogroup assignment. Y chromosome haplotype reference database wikipedia. Haplotyping programs section on statistical genetics. The task often arises to compare the spectrum of haplotypes in individuals or entire populations. In this study, 25 y chromosome single nucleotide polymorphism markers and 17 y chromosome short tandem repeat y str loci were genotyped in 1,108 males from several populations in east asia. Ychromosome haplotype strata in anatolia full article. A comparative analysis of y chromosome and mtdna phylogenies.
Worldwide repository of over 6,000 9locus, over 84,000 17locus, over 25,000 23locus haplotypes and 15,000 y snp profiles from 917 sampling locations in 128 countries. Out of an original sample of eritrean males screened, 39. In order to evaluate the genetic structure of purebred dogs, six y chromosome microsatellite markers were used to analyze dna samples from 824 unrelated dogs from 50 recognized breeds. Performing this task manually is too laborious and thus unrealistic.
In the present study, through extensive sampling of east asian populations and genotyping of y chromosome markers snps and strs that define an east asianspecific y chromosome haplogroup o3m122we intended to delineate the origin of the o3m122 haplogroup, to shed more light on the prehistoric migration of modern humans in east asia. Several authors have proposed haplotype motifs based on site variants at the mitochondrial genome mtdna and the nonrecombining portion of the y chromosome nry to trace the genealogies of jewish people. The objective of this research was to contribute to a better characterisation of the brazilian population genetic structure. Abstract analysis of 89 biallelic polymorphisms in 523 turkish y chromosomes revealed 52 distinct haplotypes with considerable haplogroup substructure, as exemplified by their respective levels of accumulated diversity at ten short tandem repeat str loci. Allele frequencies of 36 ystr loci and haplotype frequencies were calculated using the direct counting method. The web edition of the y dna haplogroup predictor was made by milos cetkovic gentula and aco nevski, under the auspices of the serbian dna project, 2015.
High frequencies of ychromosome haplogroup o2bsry465. Genetic analyzer applied biosystems, weiterstadt, germany and the genotyper software. Y chromosome haplotype analysis in purebred dogs uc davis. Wes chromosome y offtarget reads coverage compare to autosome hi all, i have couple of wes samples using different capture kits, and would like to predict thei. In many polymorphic regions, the density of differences can be as high as 1 per 10 bases when different haplotypes are compared but as low as 0 if the haplotypes are the same.
Multinomial model as in em algorithm for individual haplotypes. For details see the paper by ralf et al 2018 yleaf. Other applications for y strs include tracing paternal lineages to aid in missing persons investigations and historical studies and to help link families through genetic genealogy. Conversion of absolute fragment size to number of allele repeats was. I need information about analyzing y chromosome strs data. I discuss here basic principles in using yhaplotype information for identity or paternity. However, unlike for autosomal profiles, the problem of evaluating weightofevidence for y profiles has not been satisfactorily resolved despite many attempts. Simultaneous analysis of hundreds of ychromosomal snps.
Y str haplotype reference database yhrd is a searchable worldwide database of y str haplotypes in various formats along with tools build upon their distribution. Famhap famhap is a software for singlemarker analysis and, in particular, joint analysis of unphased genotype data from tightly linked markers haplotype analysis. Y dna str testing will provide a haplogroup estimate, while the more intensive y dna snp test provides a definitive haplogroup. Y dna test results also involve haplogroups, which can help determine what particular line of the human ancestral dna tree a testtakers y chromosome originates from. Y chromosomal haplogroup g1 is a minor component of the overall gene pool of southwest and central asia but reaches up to 80% frequency in some populations scattered within this area. Haplogroup short form, with the name of a representative snp. In these cases, the genotype is 46, xx this would normally indicate a female genotype. Ychromosome polymorphisms and ethnic group a combined str and snp approach in a population sample from northern italy. The main advantage of this software is that the analysis is performed based on the frequency of haplotypes, which was identified by combining the size variants at the. The results that comprise the full ydna haplotype from the y chromosome dna test can be divided into two parts. The analysis of y chromosome haplotypes can thus provide additional. Short tandem repeats str and singlenucleotide polymorphisms snp on the y chromosome were typed in 311 unrelated men from four different ethnic groups italians from northern italy, albanians, africans from the maghreb region, and indopakistanis, using the ampflstr yfiler pcr amplification kit and the snapshot multiplex kit. A global analysis of ychromosomal haplotype diversity for 23 str loci. To our knowledge, extended y chromosome haplotypes that combine information from strs and snps have not been used to.
Frontiers mitochondrial and y chromosome haplotype. Yfitter is a program for assigning y chromosome haplogroups to individuals sequenced at low coverage. Analysis of y chromosome snps in alagoas, northeastern. Population data was obtained from a sample of 400 unrelated individuals living in antioquia colombia. Yleaf a tool for performing haplogroup predictions from next generation sequencing data bam or fastq files. Haplogroup long form, using ychromosome consortium nomenclature. In general, we found east asian populations to be characterized by male haplogroup homogeneity, showing major y chromosomal expansions of haplogroup o. For forensic labs, the most common application of y strs is in criminal cases such as sexual assault, where evidence samples are difficult to resolve with traditional autosomal str analysis due to low amounts of male dna present in a high background of female dna. Comparison of phylogenies inferred from dna sequences with differing inheritance patterns, such as mitochondrial, autosomal, and x and y chromosomal loci, can provide more comprehensive.
A first ychromosomal haplotype network to investigate. Ychromosome strs are demonstrating value in the forensic identification of male dna from sexual assault cases. Ychromosomal snp haplotype diversity in forensic analysis. Allele frequencies and haplotype analysis have been performed for eight y chromosome strs dys19, dys385 i and ii, dys389 i and ii, dys390, dys391, dys392, dys393.
Deep phylogenetic analysis of haplogroup g1 provides. In designing better algorithms, the strategy for comparative analysis will be crucial. The original scientific research was based on the hypothesis that a majority of presentday jewish kohanim share a pattern of values for six ystr markers, which researchers named the cohen modal haplotype. Here, we analyzed their main approaches and test the feasibility of adopting motifs as ancestry markers through construction of a large database of mtdna and nry haplotypes from public. A relatively small number of haplotypes 67 were identified in this large sample set due to extensive sharing of haplotypes between breeds and low haplotype diversity within breeds. Here is a list of y chromosome and mtdna geographic haplogroup assignation proposed by bekada et al. Haplotype is a contraction for haploid genotype it refers to a collection of specific alleles in a cluster of tightlylinked genes. Mitochondrial and y chromosome haplotype motifs as diagnostic. Str haplotypes of the y chromosome are widely used as effective genetic markers in studies of human populations and in forensic dna analysis. Genetic distance between the five studied ethnic groups and other published groups was analyzed by analysis of molecular variance and visualized in a multidimensional scaling plot.
According to the hebrew bible, this ancestor was aaron, the brother of moses. Y chromosome haplotype analysis in portuguese cattle breeds. The haplotypes were transferred to excel software for data analysis. Ychromosomal str haplotype analysis reveals surname. This represents a major contrast with autosomal profiles, the implications of which have not been fully addressed 2. All groups exhibited high haplotype diversities but low interpopulation variance as measured by an analysis of molecular variance. Put in simple words, haplotype is the group of genes that a progeny inherits from one parent. Haplotype phase inference software tools population genetics data analysis two categories of computational methods exist for determining haplotypes. Ystr haplotype reference database yhrd is a searchable worldwide database of ystr haplotypes in various formats along with tools build upon their. Abstractforensic haplotype analysis of the male y chromosome is. Y chromosome haplotype analysis in portuguese cattle. Haploblock is suitable for high density haplotype or genotype snp marker data. Haploview currently supports the following functionalities. Ninety different haplotypes were obtained from 99 unrelated szekely males.
Haplotype analysis is a new software for analysis of data from organelle genomes chloroplast or mitochondrial which are observed from microsatellites ssr or pcrrflp markers. It follows that analysis without haplotype assignment will be misleading. Jul 14, 2005 in the present study, through extensive sampling of east asian populations and genotyping of ychromosome markers snps and strs that define an east asianspecific ychromosome haplogroupo3m122we intended to delineate the origin of the o3m122 haplogroup, to shed more light on the prehistoric migration of modern humans in east asia. The tighter the linkage, the less likely that the collection of alleles will be broken up by recombination.
Ychromosome polymorphisms and ethnic group a combined. Several commercial organizations now offer haplotype analysis. At analysis of y chromosome microsatellites according to bannasch et al. A haplotype greek haploos simple is the genetic constitution of an individual chromosome.