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Statistical and computational genetics

This section incorporates all aspects of statistical and computational genetics, including but not limited to: methods and applications for the analysis of all types of genetic data.

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  1. The genetic variants identified by Genome-wide association study (GWAS) can only account for a small proportion of the total heritability for complex disease. The existence of gene-gene joint effects which con...

    Authors: Jing Xu, Zhongshang Yuan, Jiadong Ji, Xiaoshuai Zhang, Hongkai Li, Xuesen Wu, Fuzhong Xue and Yanxun Liu

    Citation: BMC Genetics 2016 17:31

    Content type: Methodology article

    Published on:

  5. In recent years, with the development of high-throughput sequencing technology and the commercial availability of genotyping bead chips, more attention is being directed towards the utilization of abundant gen...

    Authors: Ning Gao, Jiaqi Li, Jinlong He, Guang Xiao, Yuanyu Luo, Hao Zhang, Zanmou Chen and Zhe Zhang

    Citation: BMC Genetics 2015 16:120

    Content type: Methodology article

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  6. A complete approach for genome-wide selection (GWS) involves reliable statistical genetics models and methods. Reports on this topic are common for additive genetic models but not for additive-dominance models...

    Authors: Camila Ferreira Azevedo, Marcos Deon Vilela de Resende, Fabyano Fonseca e Silva, José Marcelo Soriano Viana, Magno Sávio Ferreira Valente, Márcio Fernando Ribeiro Resende Jr and Patricio Muñoz

    Citation: BMC Genetics 2015 16:105

    Content type: Methodology article

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  8. Genotype imputation is a common technique in genetic research. Genetic similarity between target population and reference dataset is crucial for high-quality results. Although several reference panels are avai...

    Authors: Nab Raj Roshyara and Markus Scholz

    Citation: BMC Genetics 2015 16:90

    Content type: Research article

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  9. Accurate genotype imputation can greatly reduce costs and increase benefits by combining whole-genome sequence data of varying read depth and array genotypes of varying densities. For large populations, an eff...

    Authors: Paul M. VanRaden, Chuanyu Sun and Jeffrey R. O’Connell

    Citation: BMC Genetics 2015 16:82

    Content type: Research article

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  10. Strategies for imputing genotypes from the Illumina-Bovine3K, Illumina-BovineLD (6K), BeefLD-GGP (8K), a non-commercial-15K and IndicusLD-GGP (20K) to either Illumina-BovineSNP50 (50K) or to Illumina-BovineHD ...

    Authors: Mario L Piccoli, José Braccini, Fernando F Cardoso, Medhi Sargolzaei, Steven G Larmer and Flávio S Schenkel

    Citation: BMC Genetics 2014 15:157

    Content type: Research article

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  11. Genome-wide Association Studies (GWAS) are typically designed to identify phenotype-associated single nucleotide polymorphisms (SNPs) individually using univariate analysis methods. Though providing valuable insi...

    Authors: Xiaoshuai Zhang, Fuzhong Xue, Hong Liu, Dianwen Zhu, Bin Peng, Joseph L Wiemels and Xiaowei Yang

    Citation: BMC Genetics 2014 15:130

    Content type: Research article

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  15. Two genetic marker-based methods are compared for use in breed prediction, using a New Zealand sheep resource. The methods were a genomic selection (GS) method, using genomic BLUP, and a regression method (Reg...

    Authors: Ken G Dodds, Benoît Auvray, Sheryl-Anne N Newman and John C McEwan

    Citation: BMC Genetics 2014 15:92

    Content type: Research article

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  16. Imputation of partially missing or unobserved genotypes is an indispensable tool for SNP data analyses. However, research and understanding of the impact of initial SNP-data quality control on imputation resul...

    Authors: Nab Raj Roshyara, Holger Kirsten, Katrin Horn, Peter Ahnert and Markus Scholz

    Citation: BMC Genetics 2014 15:88

    Content type: Research article

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  17. Cox-regression-based methods have been commonly used for the analyses of survival outcomes, such as age-at-disease-onset. These methods generally assume the hazard functions are proportional among various risk...

    Authors: Ming Li, Joseph C Gardiner, Naomi Breslau, James C Anthony and Qing Lu

    Citation: BMC Genetics 2014 15:79

    Content type: Methodology article

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  20. The expense of human leukocyte antigen (HLA) allele genotyping has motivated the development of imputation methods that use dense single nucleotide polymorphism (SNP) genotype data and the region’s haplotype stru...

    Authors: Albert M Levin, Indra Adrianto, Indrani Datta, Michael C Iannuzzi, Sheri Trudeau, Paul McKeigue, Courtney G Montgomery and Benjamin A Rybicki

    Citation: BMC Genetics 2014 15:72

    Content type: Research article

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  21. Maternal-fetal genotype incompatibility (MFGI) is increasingly reported to influence human diseases, especially pregnancy-related complications. In practice, it is challenging to identify the ideal incompatibi...

    Authors: Shaoyu Li, Yuehua Cui and Roberto Romero

    Citation: BMC Genetics 2014 15:66

    Content type: Research article

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  22. Genome-wide scans for regions that demonstrate deviating patterns of genetic variation have become common approaches for finding genes targeted by selection. Several genomic patterns have been utilized for thi...

    Authors: Agnès E Sjöstrand, Per Sjödin and Mattias Jakobsson

    Citation: BMC Genetics 2014 15:61

    Content type: Methodology article

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  24. In genetic analysis of agronomic traits, quantitative trait loci (QTLs) that control the same phenotype are often closely linked. Furthermore, many QTLs are localized in specific genomic regions (QTL clusters)...

    Authors: Eiji Yamamoto, Hiroyoshi Iwata, Takanari Tanabata, Ritsuko Mizobuchi, Jun-ichi Yonemaru, Toshio Yamamoto and Masahiro Yano

    Citation: BMC Genetics 2014 15:50

    Content type: Methodology article

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  27. Association mapping studies offer great promise to identify polymorphisms associated with phenotypes and for understanding the genetic basis of quantitative trait variation. To date, almost all association map...

    Authors: Abdoul-Aziz Saïdou, Anne-Céline Thuillet, Marie Couderc, Cédric Mariac and Yves Vigouroux

    Citation: BMC Genetics 2014 15:3

    Content type: Research article

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  30. Risk prediction models capitalizing on genetic and environmental information hold great promise for individualized disease prediction and prevention. Nevertheless, linking the genetic and environmental risk pr...

    Authors: Chengyin Ye and Qing Lu

    Citation: BMC Genetics 2013 14:122

    Content type: Software

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  31. MicroRNAs (miRNAs) regulate many biological processes by post-translational gene silencing. Analysis of miRNA expression profiles is a reliable method for investigating particular biological processes due to t...

    Authors: Bo Sun, Fei Yang, Fei-Hu Hu, Ning-Ping Huang and Zhong-Dang Xiao

    Citation: BMC Genetics 2013 14:120

    Content type: Methodology article

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  32. Identification of true to breed type animal for conservation purpose is imperative. Breed dilution is one of the major problems in sustainability except cases of commercial crossbreeding under controlled condi...

    Authors: Mir Asif Iquebal, Sarika, Sandeep Kumar Dhanda, Vasu Arora, Sat Pal Dixit, Gajendra PS Raghava, Anil Rai and Dinesh Kumar

    Citation: BMC Genetics 2013 14:118

    Content type: Software

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  33. The advent of genome-wide association studies has led to many novel disease-SNP associations, opening the door to focused study on their biological underpinnings. Because of the importance of analyzing these a...

    Authors: David M Swanson, Deborah Blacker, Taofik AlChawa, Kerstin U Ludwig, Elisabeth Mangold and Christoph Lange

    Citation: BMC Genetics 2013 14:108

    Content type: Methodology article

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  34. On thinking quantitatively of complex diseases, there are at least three statistical strategies for analyzing the gene-gene interaction: SNP by SNP interaction on single trait, gene-gene (each can involve mult...

    Authors: Fangyu Li, Jinghua Zhao, Zhongshang Yuan, Xiaoshuai Zhang, Jiadong Ji and Fuzhong Xue

    Citation: BMC Genetics 2013 14:89

    Content type: Research article

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  35. Pooling is a cost effective way to collect data for genetic association studies, particularly for rare genetic variants. It is of interest to estimate the haplotype frequencies, which contain more information ...

    Authors: Anthony YC Kuk, Xiang Li and Jinfeng Xu

    Citation: BMC Genetics 2013 14:82

    Content type: Methodology article

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  36. In cross breeding, it is important to choose a good parental combination that has high probability of generating offspring with desired characteristics. This study examines a method for predicting the segregat...

    Authors: Hiroyoshi Iwata, Takeshi Hayashi, Shingo Terakami, Norio Takada, Toshihiro Saito and Toshiya Yamamoto

    Citation: BMC Genetics 2013 14:81

    Content type: Methodology article

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  37. Triad families are routinely used to test association between genetic variants and complex diseases. Triad studies are important and popular since they are robust in terms of being less prone to false positive...

    Authors: Ruzong Fan, Annie Lee, Zhaohui Lu, Aiyi Liu, James F Troendle and James L Mills

    Citation: BMC Genetics 2013 14:78

    Content type: Methodology article

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  40. We address the task of extracting accurate haplotypes from genotype data of individuals of large F1 populations for mapping studies. While methods for inferring parental haplotype assignments on large F1 populati...

    Authors: Filippo Utro, Niina Haiminen, Donald Livingstone III, Omar E Cornejo, Stefan Royaert, Raymond J Schnell, Juan Carlos Motamayor, David N Kuhn and Parida Laxmi

    Citation: BMC Genetics 2013 14:48

    Content type: Methodology article

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  42. F2 resource populations have been used extensively to map QTL segregating between pig breeds. A limitation associated with the use of these resource populations for fine mapping of QTL is the reduced number of f....

    Authors: Jose L Gualdrón Duarte, Ronald O Bates, Catherine W Ernst, Nancy E Raney, Rodolfo JC Cantet and Juan P Steibel

    Citation: BMC Genetics 2013 14:38

    Content type: Research article

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  46. For genetic association studies in designs of unrelated individuals, current statistical methodology typically models the phenotype of interest as a function of the genotype and assumes a known statistical mod...

    Authors: Sharon Lutz, Wai-Ki Yip, John Hokanson, Nan Laird and Christoph Lange

    Citation: BMC Genetics 2013 14:13

    Content type: Methodology article

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  47. Recombination rates vary at the level of the species, population and individual. Now recognized as a transient feature of the genome, recombination rates at a given locus can change markedly over time. Existin...

    Authors: Murray P Cox, Barbara R Holland, Matthew C Wilkins and Jan Schmid

    Citation: BMC Genetics 2013 14:11

    Content type: Research article

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  48. Genotype imputation is a cost efficient alternative to use of high density genotypes for implementing genomic selection. The objective of this study was to investigate variables affecting imputation accuracy f...

    Authors: Yvonne M Badke, Ronald O Bates, Catherine W Ernst, Clint Schwab, Justin Fix, Curtis P Van Tassell and Juan P Steibel

    Citation: BMC Genetics 2013 14:8

    Content type: Research article

    Published on:

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