一种用于快速计算同一性系数和广义亲属系数的图形算法。
A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients.
作者信息
Abney Mark
机构信息
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
出版信息
Bioinformatics. 2009 Jun 15;25(12):1561-3. doi: 10.1093/bioinformatics/btp185. Epub 2009 Apr 9.
Abstract
UNLABELLED
Computing the probability of identity by descent sharing among n genes given only the pedigree of those genes is a computationally challenging problem, if n or the pedigree size is large. Here, I present a novel graphical algorithm for efficiently computing all generalized kinship coefficients for n genes. The graphical description transforms the problem from doing many recursion on the pedigree to doing a single traversal of a structure referred to as the kinship graph.
AVAILABILITY
The algorithm is implemented for n = 4 in the software package IdCoefs at http://home.uchicago.edu/abney/Software.html.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
未标注
仅根据基因的系谱计算n个基因之间通过血缘共享的同一性概率，若n或系谱规模较大，则是一个计算上具有挑战性的问题。在此，我提出一种新颖的图形算法，用于高效计算n个基因的所有广义亲属系数。这种图形描述将问题从在系谱上进行多次递归转换为对一种称为亲属关系图的结构进行单次遍历。
可用性
该算法已在http://home.uchicago.edu/abney/Software.html的软件包IdCoefs中针对n = 4实现。
联系方式
补充信息
补充数据可在《生物信息学》在线获取。
相似文献
1
A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients.一种用于快速计算同一性系数和广义亲属系数的图形算法。
Bioinformatics. 2009 Jun 15;25(12):1561-3. doi: 10.1093/bioinformatics/btp185. Epub 2009 Apr 9.
2
Efficient computation of kinship and identity coefficients on large pedigrees.大型家系中亲缘系数和同一性系数的高效计算。
J Bioinform Comput Biol. 2009 Jun;7(3):429-53. doi: 10.1142/s0219720009004175.
3
Efficient computation of the kinship coefficients.高效计算亲缘系数。
Bioinformatics. 2019 Mar 15;35(6):1002-1008. doi: 10.1093/bioinformatics/bty725.
4
Scalable computation of kinship and identity coefficients on large pedigrees.在大型谱系上可扩展地计算亲缘系数和同一性系数。
Comput Syst Bioinformatics Conf. 2008;7:27-36.
5
Path-counting formulas for generalized kinship coefficients and condensed identity coefficients.广义亲缘系数和压缩恒同系数的路径计数公式。
Comput Math Methods Med. 2014;2014:898424. doi: 10.1155/2014/898424. Epub 2014 Jul 21.
6
IBDkin: fast estimation of kinship coefficients from identity by descent segments.IBDkin：基于降同关系片段的亲缘系数快速估计
Bioinformatics. 2020 Aug 15;36(16):4519-4520. doi: 10.1093/bioinformatics/btaa569.
7
Probability of gene identity by descent: computation and applications.基于家系的基因同一性概率：计算与应用
Biometrics. 1994 Mar;50(1):109-17.
8
FamSeq: a variant calling program for family-based sequencing data using graphics processing units.FamSeq：一种使用图形处理单元处理基于家系测序数据的变异检测程序。
PLoS Comput Biol. 2014 Oct 30;10(10):e1003880. doi: 10.1371/journal.pcbi.1003880. eCollection 2014 Oct.
9
Stochastic simulation GUI for biochemical networks.用于生化网络的随机模拟图形用户界面。
Bioinformatics. 2007 Jul 15;23(14):1859-61. doi: 10.1093/bioinformatics/btm231. Epub 2007 Jun 22.
10
Numericware N: Numerator Relationship Matrix Calculator.Numericware N：分子关系矩阵计算器。
J Hered. 2016;107(7):686-690. doi: 10.1093/jhered/esw057. Epub 2016 Oct 11.
引用本文的文献
1
Estimation of Jacquard's genetic identity coefficients with bi-allelic variants by constrained least-squares.通过约束最小二乘法利用双等位基因变异估计雅卡尔遗传同一性系数。
Heredity (Edinb). 2025 Jan;134(1):10-20. doi: 10.1038/s41437-024-00731-z. Epub 2024 Nov 7.
2
Ballou's Ancestral Inbreeding Coefficient: Formulation and New Estimate with Higher Reliability.巴卢的祖先近亲繁殖系数：公式及更高可靠性的新估计值。
Animals (Basel). 2024 Jun 21;14(13):1844. doi: 10.3390/ani14131844.
3
The infinitesimal model with dominance.具有显性的无穷小模型
Genetics. 2023 Oct 4;225(2). doi: 10.1093/genetics/iyad133.
4
QuickPed: an online tool for drawing pedigrees and analysing relatedness.QuickPed：一个用于绘制系谱图和分析亲缘关系的在线工具。
BMC Bioinformatics. 2022 Jun 7;23(1):220. doi: 10.1186/s12859-022-04759-y.
6
Relatedness coefficients in pedigrees with inbred founders.系谱中近交系创始人的相关系数。
J Math Biol. 2020 Jul;81(1):185-207. doi: 10.1007/s00285-020-01505-x. Epub 2020 Jun 8.
7
Quantitative analysis of population-scale family trees with millions of relatives.对包含数百万亲属的大规模家族树进行定量分析。
Science. 2018 Apr 13;360(6385):171-175. doi: 10.1126/science.aam9309. Epub 2018 Mar 1.
8
Genotype-Based Score Test for Association Testing in Families.基于基因型的家系关联检验得分检验
Stat Biosci. 2015;7(2):394-416. doi: 10.1007/s12561-015-9128-6. Epub 2015 Mar 17.
9
A novel recursive algorithm for the calculation of the detailed identity coefficients.一种用于计算详细亲缘系数的新型递归算法。
Genet Sel Evol. 2015 Apr 29;47(1):33. doi: 10.1186/s12711-015-0108-6.
10
Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness.在存在亲缘关系的情况下，对群体结构进行稳健推断，以进行血统预测和分层校正。
Genet Epidemiol. 2015 May;39(4):276-93. doi: 10.1002/gepi.21896. Epub 2015 Mar 23.
本文引用的文献
1
Scalable computation of kinship and identity coefficients on large pedigrees.在大型谱系上可扩展地计算亲缘系数和同一性系数。
Comput Syst Bioinformatics Conf. 2008;7:27-36.
2
Homozygosity by descent mapping of blood pressure in the Old Order Amish: evidence for sex specific genetic architecture.老派阿米什人血压的纯合子定位：性别特异性遗传结构的证据
BMC Genet. 2007 Oct 1;8:66. doi: 10.1186/1471-2156-8-66.
3
Patterns of linkage disequilibrium between SNPs in a Sardinian population isolate and the selection of markers for association studies.撒丁岛人群隔离群体中 SNPs 之间的连锁不平衡模式及关联研究标记的选择
Hum Hered. 2008;65(1):9-22. doi: 10.1159/000106058. Epub 2007 Jul 25.
4
The sex-specific genetic architecture of quantitative traits in humans.人类数量性状的性别特异性遗传结构。
Nat Genet. 2006 Feb;38(2):218-22. doi: 10.1038/ng1726. Epub 2006 Jan 22.
5
Testing for Hardy-Weinberg equilibrium in samples with related individuals.在有亲属关系个体的样本中进行哈迪-温伯格平衡检验。
Genetics. 2004 Dec;168(4):2349-61. doi: 10.1534/genetics.104.031617. Epub 2004 Sep 15.
6
GENOTYPIC COVARIANCES BETWEEN INBRED RELATIVES.近交亲属间的基因型协方差。
Genetics. 1964 Dec;50(6):1319-48. doi: 10.1093/genetics/50.6.1319.
7
A recursive algorithm for the calculation of identity coefficients.一种用于计算同一性系数的递归算法。
Ann Hum Genet. 1981 Jul;45(3):299-305. doi: 10.1111/j.1469-1809.1981.tb00341.x.
8
Gene identities and multiple relationships.基因身份与多重关系。
Biometrics. 1974 Dec;30(4):667-80.
9
The affected-pedigree-member method of linkage analysis.连锁分析的受累家系成员法。
Am J Hum Genet. 1988 Feb;42(2):315-26.
10
Calculation of genetic identity coefficients.遗传同一性系数的计算。
Ann Hum Genet. 1992 Oct;56(4):339-46. doi: 10.1111/j.1469-1809.1992.tb01162.x.
Zotero 插件