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Statistical and computational genetics

Section edited by Rongling Wu

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. Content type: Research article

    Various biological materials unrelated to humans are found at crime scenes and it is often important to elucidate the origin of these materials. A genetic locus common to several species is conventionally PCR-...

    Authors: Takako Kinebuchi, Nozomi Idota, Hajime Tsuboi, Marin Takaso, Risa Bando and Hiroshi Ikegaya

    Citation: BMC Genetics 2019 20:50

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  2. Content type: Research article

    It becomes clear that the increase in the density of marker panels and even the use of sequence data didn’t result in any meaningful increase in the accuracy of genomic selection (GS) using either regression (...

    Authors: Ling-Yun Chang, Sajjad Toghiani, Samuel E. Aggrey and Romdhane Rekaya

    Citation: BMC Genetics 2019 20:21

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  3. Content type: Research article

    Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA ba...

    Authors: Prabina Kumar Meher, Tanmaya Kumar Sahu, Shachi Gahoi, Ruchi Tomar and Atmakuri Ramakrishna Rao

    Citation: BMC Genetics 2019 20:2

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  4. Content type: Methodology article

    X chromosome inactivation (XCI) is an important gene regulation mechanism in females to equalize the expression levels of X chromosome between two sexes. Generally, one of two X chromosomes in females is rando...

    Authors: Si-Qi Xu, Yu Zhang, Peng Wang, Wei Liu, Xian-Bo Wu and Ji-Yuan Zhou

    Citation: BMC Genetics 2018 19:109

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  5. Content type: Research article

    SNPs are informative to estimate genomic breed composition (GBC) of individual animals, but selected SNPs for this purpose were not made available in the commercial bovine SNP chips prior to the present study....

    Authors: Jun He, Yage Guo, Jiaqi Xu, Hao Li, Anna Fuller, Richard G. Tait Jr, Xiao-Lin Wu and Stewart Bauck

    Citation: BMC Genetics 2018 19:56

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  6. Content type: Research article

    The central tenet of ‘genome content’ has been that the ‘non-coding’ parts are highly enriched with ‘microsatellites’ or ‘Simple Sequence Repeats’ (SSRs). We presume that the presence and change in number of r...

    Authors: Nisha Joy, Y. P. Maimoonath Beevi and E. V. Soniya

    Citation: BMC Genetics 2018 19:29

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  7. Content type: Research article

    The availability of high-density (HD) marker panels, genome wide variants and sequence data creates an unprecedented opportunity to dissect the genetic basis of complex traits, enhance genomic selection (GS) a...

    Authors: Ling-Yun Chang, Sajjad Toghiani, Ashley Ling, Sammy E. Aggrey and Romdhane Rekaya

    Citation: BMC Genetics 2018 19:4

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    The Correction to this article has been published in BMC Genetics 2018 19:13

  8. Content type: Methodology article

    Weighted genetic risk scores (GRS), defined as weighted sums of risk alleles of single nucleotide polymorphisms (SNPs), are statistically powerful for detection gene-environment (GxE) interactions. To assign w...

    Authors: Anke Hüls, Ursula Krämer, Christopher Carlsten, Tamara Schikowski, Katja Ickstadt and Holger Schwender

    Citation: BMC Genetics 2017 18:115

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  9. Content type: Research article

    Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil pa...

    Authors: Qi Bin Kwong, Chee Keng Teh, Ai Ling Ong, Fook Tim Chew, Sean Mayes, Harikrishna Kulaveerasingam, Martti Tammi, Suat Hui Yeoh, David Ross Appleton and Jennifer Ann Harikrishna

    Citation: BMC Genetics 2017 18:107

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  10. Content type: Methodology article

    When testing for SNP (single nucleotide polymorphism) associations in related individuals, observations are not independent. Simple linear regression assuming independent normally distributed residuals results...

    Authors: Arnd Gross, Anke Tönjes and Markus Scholz

    Citation: BMC Genetics 2017 18:104

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  11. Content type: Methodology article

    Undirected graphical models or Markov random fields have been a popular class of models for representing conditional dependence relationships between nodes. In particular, Markov networks help us to understand...

    Authors: Hosik Choi, Jungsoo Gim, Sungho Won, You Jin Kim, Sunghoon Kwon and Changyi Park

    Citation: BMC Genetics 2017 18:93

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  12. Content type: Methodology article

    For dichotomous traits, the generalized disequilibrium test with the moment estimate of the variance (GDT-ME) is a powerful family-based association method. Genomic imprinting is an important epigenetic phenom...

    Authors: Jian-Long Li, Peng Wang, Wing Kam Fung and Ji-Yuan Zhou

    Citation: BMC Genetics 2017 18:90

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  13. Content type: Research article

    Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding...

    Authors: Honglin Chen, Lixia Wang, Xiaoyan Liu, Liangliang Hu, Suhua Wang and Xuzhen Cheng

    Citation: BMC Genetics 2017 18:65

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  14. Content type: Methodology article

    For the analysis of gene-environment (GxE) interactions commonly single nucleotide polymorphisms (SNPs) are used to characterize genetic susceptibility, an approach that mostly lacks power and has poor reprodu...

    Authors: Anke Hüls, Katja Ickstadt, Tamara Schikowski and Ursula Krämer

    Citation: BMC Genetics 2017 18:55

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    The Erratum to this article has been published in BMC Genetics 2017 18:73

  15. Content type: Methodology article

    Over the past decades, the prevalence of type 2 diabetes mellitus (T2D) has been steadily increasing around the world. Despite large efforts devoted to better understand the genetic basis of the disease, the i...

    Authors: Jie Ren, Tao He, Ye Li, Sai Liu, Yinhao Du, Yu Jiang and Cen Wu

    Citation: BMC Genetics 2017 18:44

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  16. Content type: Research article

    Most genome-wide association studies assumed an additive model of inheritance which may result in significant loss of power when there is a strong departure from additivity. The General Regression Model (GRM),...

    Authors: Marie-Hélène Dizier, Florence Demenais and Flavie Mathieu

    Citation: BMC Genetics 2017 18:24

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  17. Content type: Methodology article

    The evaluation and interpretation of forensic DNA mixture evidence faces greater interpretational challenges due to increasingly complex mixture evidence. Such challenges include: casework involving low quanti...

    Authors: Frederick R. Bieber, John S. Buckleton, Bruce Budowle, John M. Butler and Michael D. Coble

    Citation: BMC Genetics 2016 17:125

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  18. Content type: Research article

    mRNA expression in a cell or subcellular organelle is precisely regulated for the purpose of gene function regulation. The 3’ untranslated region (3’UTR) of mRNA is the binding target of microRNA and RNA bindi...

    Authors: Tian Li, Yaoyun Kuang and Bin Li

    Citation: BMC Genetics 2016 17:111

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  19. Content type: Research article

    Japanese larch (Larix kaempferi) as a successful exotic species has become one of the most important economic and ecological conifers in China. In order to broaden the genetic resource of Larix kaempferi, an effo...

    Authors: Shu Diao, Yimei Hou, Yunhui Xie and Xiaomei Sun

    Citation: BMC Genetics 2016 17:104

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  20. Content type: Research article

    Lynch syndrome is a hereditary cancer syndrome associated with high risks of colorectal and endometrial cancer that is caused by pathogenic variants in the mismatch repair genes (MLH1, MSH2, MSH6, PMS2, EPCAM). A...

    Authors: Brian Morris, Elisha Hughes, Eric Rosenthal, Alexander Gutin and Karla R. Bowles

    Citation: BMC Genetics 2016 17:99

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  21. Content type: Software

    Determination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and quantitative trait loci (QTL) mapping, gene...

    Authors: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar and Juan Zalapa

    Citation: BMC Genetics 2016 17:62

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  22. Content type: Methodology article

    We propose a novel Markov Blanket-based repeated-fishing strategy (MBRFS) in attempt to increase the power of existing Markov Blanket method (DASSO-MB) and maintain its advantages in omic data analysis.

    Authors: Hongkai Li, Zhongshang Yuan, Jiadong Ji, Jing Xu, Tao Zhang, Xiaoshuai Zhang and Fuzhong Xue

    Citation: BMC Genetics 2016 17:51

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  23. Content type: Methodology Article

    Core collections are important tools in genetic resources research and administration. At present, most core collection selection criteria are based on one of the following item characteristics: passport data,...

    Authors: Ernesto Borrayo, Ryoko Machida-Hirano, Masaru Takeya, Makoto Kawase and Kazuo Watanabe

    Citation: BMC Genetics 2016 17:42

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  24. Content type: Methodology article

    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

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  25. Content type: Methodology article

    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

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  26. Content type: Methodology article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Research article

    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

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  30. Content type: Research article

    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

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  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Methodology article

    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

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  34. Content type: Research article

    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

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  35. Content type: Research article

    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

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