scholarly journals Screening for Recently Selected Alleles by Analysis of Human Haplotype Similarity

2006 ◽  
Vol 78 (1) ◽  
pp. 153-159 ◽  
Author(s):  
Neil A. Hanchard ◽  
Kirk A. Rockett ◽  
Chris Spencer ◽  
Graham Coop ◽  
Margaret Pinder ◽  
...  
Keyword(s):  
Haplotype Similarity

scholarly journals Classical sickle beta-globin haplotypes exhibit a high degree of long-range haplotype similarity in African and Afro-Caribbean populations

BMC Genetics ◽  
2007 ◽  
Vol 8 (1) ◽  
Author(s):  
Neil Hanchard ◽  
Abier Elzein ◽  
Clare Trafford ◽  
Kirk Rockett ◽  
Margaret Pinder ◽  
...  
Keyword(s):  
Long Range ◽  
Beta Globin ◽  
High Degree ◽  
Haplotype Similarity ◽  
Caribbean Populations

A Haplotype Similarity Based Transmission/Disequilibrium Test under Founder Heterogeneity

2005 ◽  
Vol 69 (4) ◽  
pp. 455-467 ◽  
Author(s):  
Kai Yu ◽  
Shuanglin Zhang ◽  
Ingrid Borecki ◽  
Aldi Kraja ◽  
Chengjie Xiong ◽  
...  
Keyword(s):  
Transmission Disequilibrium Test ◽  
Transmission Disequilibrium ◽  
Haplotype Similarity

scholarly journals Comparison of measures for haplotype similarity

2007 ◽  
Vol 1 (Suppl 1) ◽  
pp. S128 ◽  
Author(s):  
Vivien Marquard ◽  
Lars Beckmann ◽  
Justo L Bermejo ◽  
Christine Fischer ◽  
Jenny Chang-Claude
Keyword(s):  
Haplotype Similarity

A new association test using haplotype similarity

2007 ◽  
Vol 31 (6) ◽  
pp. 577-593 ◽  
Author(s):  
Qiuying Sha ◽  
Huann-Sheng Chen ◽  
Shuanglin Zhang
Keyword(s):  
Association Test ◽  
New Association ◽  
Haplotype Similarity

INCREASING POWER BY USING HAPLOTYPE SIMILARITY IN A MULTIMARKER TRANSMISSION/DISEQUILIBRIUM TEST

2013 ◽  
Vol 11 (02) ◽  
pp. 1250014 ◽  
Author(s):  
MARÍA M. ABAD-GRAU ◽  
NURIA MEDINA-MEDINA ◽  
SERAFÍN MORAL ◽  
ROSANA MONTES-SOLDADO ◽  
SERGIO TORRES-SÁNCHEZ ◽  
...  
Keyword(s):  
High Risk ◽  
Prior Knowledge ◽  
Transmission Disequilibrium Test ◽  
State Of The Art ◽  
Real Data ◽  
Low Risk ◽  
Data Sets ◽  
Transmission Disequilibrium ◽  
Maximum Extent ◽  
Haplotype Similarity

It is already known that power in multimarker transmission/disequilibrium tests may improve with the number of markers as some associations may require several markers to be captured. However, a mechanism such as haplotype grouping must be used to avoid incremental complexity with the number of markers. 2G, a state-of-the-art transmission/disequilibrium test, implements this mechanism to its maximum extent by grouping haplotypes into only two groups, high and low-risk haplotypes, so that the test has only one degree of freedom regardless of the number of markers. The test checks whether those haplotypes more often transmitted from parents to offspring are truly high-risk haplotypes. In this paper we use haplotype similarity as prior knowledge to classify haplotypes as high or low risk ones and start with those haplotypes in which the prior will have lower impact i.e. those with the largest differences between transmission and non-transmission counts. If their counts are very different, the prior knowledge has little effect and haplotypes are classified as low or high risk as 2G does. We show a substantial gain in power achieved by this approach, in both simulation and real data sets.

scholarly journals Applied Research of Distinguishing Similar Y-STR Haplotypes by Y Chromosome Complete Sequencing

2021 ◽  
Author(s):  
Xingyi Yang ◽  
Zhonghao Yu ◽  
Shuanglin Li ◽  
Manling Huang ◽  
Song Cai ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Liquid Phase ◽  
Y Chromosome ◽  
Close Relation ◽  
Paternal Line ◽  
Complete Sequencing ◽  
Survey Results ◽  
Haplotype Similarity ◽  
Family Investigation ◽  
Generation Sequencing

Abstract Background: To explore a technical method to distinguish similar Y-STR haplotypes and its value in deducing the differentiation the males in paternal line, we used a complete genome sequence of Y chromosome using streptavidin–biotin magnetic particle-based capture methodology (Y chromosome liquid phase probe capture next generation sequencing technique (NGS)) to detect male individuals with similar Y-STR haplotypes. Based on our independently developed mathematical model and the new topological structure of Y chromosome mutation sites as well as haplogroups and pedigree trees updated by the International Society of Genealogy (ISOGG) every year, we distinguished the coancestry of male individuals with similar Y-STR haplotypes and Results: Identifying differences between the judgment results of Y full sequencing and the pedigree survey results allowed for the estimation whether the individuals have close relation within 3~5 generations or not. Y chromosome liquid phase probe capture NGS technique could capture the 16M region and effectively analyze tens of thousands of Y-SNP loci. Among them, the coancestry obtained by analysis of 8 sample cases was consistent with the actual total case time obtained by family investigation. Conclusions: Detecting the Y-STR haplotype similarity between male individuals and conducting the previously reported mathematical model analysis by using Y chromosome liquid phase probe capture NGS technology can uncover the coancestry of the different male individuals. These results provide the foundation for further investigation of the similar Y-STR haplotype males in the Y-STR database.

scholarly journals A Regression-based Association Test for Case-control Studies that Uses Inferred Ancestral Haplotype Similarity

2009 ◽  
Vol 73 (5) ◽  
pp. 520-526 ◽  
Author(s):  
Youfang Liu ◽  
Yi-Ju Li ◽  
Glen A. Satten ◽  
Andrew S. Allen ◽  
Jung-Ying Tzeng
Keyword(s):  
Case Control ◽  
Association Test ◽  
Ancestral Haplotype ◽  
Case Control Studies ◽  
Haplotype Similarity

scholarly journals On the Identification of Disease Mutations by the Analysis of Haplotype Similarity and Goodness of Fit

2003 ◽  
Vol 72 (4) ◽  
pp. 891-902 ◽  
Author(s):  
Jung-Ying Tzeng ◽  
B. Devlin ◽  
Larry Wasserman ◽  
Kathryn Roeder
Keyword(s):  
Goodness Of Fit ◽  
Disease Mutations ◽  
Haplotype Similarity
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