Improving genomic prediction accuracy of pig reproductive traits based on genotype imputation using preselected markers with different imputation platforms by J. Sun, J. Wei, Y. Pan, M. Cao, X. Li, J. Xiao, G. Yang, T. Yu

“…In this study, the imputation from 80 k Single Nucleotide Polymorphism chip data of 832 Large White pigs to whole-genome sequencing genotypes was performed by Swine Imputation Server, Pig Haplotypes Reference Panel (PHARP), Animal Genotype Imputation Database and 1k-pig-genomes four thousand-pig imputation panels. …”
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Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds by Laura Iacolina, Astrid V. Stronen, Cino Pertoldi, Małgorzata Tokarska, Louise S. Nørgaard, Joaquin Muñoz, Anders Kjærsgaard, Aritz Ruiz-Gonzalez, Stanisław Kamiński, Deirdre C. Purfield

“…Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). …”
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Chromosome-Level Genome Assembly and Annotation of the Highly Heterozygous <i>Phallus echinovolvatus</i> Provide New Insights into Its Genetics by Mengya An, Ruoxi Liang, Yanliu Chen, Jinhua Zhang, Xiuqing Wang, Xing Li, Guohua Qu, Junfeng Liang

“…Collinear relationships were not observed for 15.38% of the genes in the two haplotypes. Hap1 had 256 unique genes, and Hap2 had 370 unique genes. …”
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Interaction Effects of Lipoprotein Lipase Polymorphisms with Lifestyle on Lipid Levels in a Korean Population: A Cross-sectional Study by Jung-A Pyun, Sunshin Kim, KyungChae Park, Inkyung Baik, Nam H Cho, InSong Koh, Jong-Young Lee, Yoon Shin Cho, Young Jin Kim, Min Jin Go, Eugene Shim, KyuBum Kwack, Chol Shin

“…The association study showed that 15 SNPs and 4 haplotypes were strongly associated with HDLC (lowest p = 2.86 × 10-22) and triglyceride levels (lowest p = 3.0 × 10-15). …”
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Tumor Necrosis Factor-Alpha Gene Promoter Region Polymorphism and the Risk of Coronary Heart Disease by Gul Zareen Asifa, Afrose Liaquat, Iram Murtaza, Syed Ali Raza Kazmi, Qamar Javed

“…There was no significant link between the −1031T>C polymorphism and CHD risk in the study population. Haplotypes A-T and A-C of the TNF-alpha gene loci at −863 and −1031 showed higher frequency in the patient group compared with controls (P<0.05). …”
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Polymorphism in the Vesicular Monoamine Transporter 2 Gene Decreases the Risk of Parkinson’s Disease in Han Chinese Men by Xinglong Yang, Pingrong Xu, Quanzhen Zhao, Ran An, Hua Jia, Zhuolin Liu, Yanming Xu

“…None of the observed haplotypes showed a significant association with PD. …”
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Some limitations in the use of the mitochondrial DNA cytb gene as a molecular marker for phylogenetic and population genetic studies by the example of the Apodemus genus by A. G. Lapinski, M. V. Pavlenko, L. L. Solovenchuk, V. V. Gorbachev

“…For this purpose, the entropy of nucleotide sequences was calculated, and probable tracts of gene conversion were sought in samples of various Apodemus species from Tibet, Korea, south of Russian Primorye, and Western Europe. Many haplotypes were identified as containing tracts of gene conversion. …”
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Matrix Gla Protein and Nitric Oxide Synthase-3 Genetic Variants in Chronic Kidney Disease and Their Relation with Cardiovascular Risk by G. Priyadarshini, Sreejith Parameswaran, Jayaprakash Sahoo, Sandhiya Selvarajan, Ananthakrishnan Ramesh, Medha Rajappa

“…We also found a significant difference in the distribution of TTA and CCG haplotypes of MGP polymorphisms (1-rs4236; 2-rs1800801; 3-rs1800802) between the groups, indicating an increase in the risk of CKD. …”
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Sources of the mitochondrial gene pool of Russians by the results of analysis of modern and paleogenomic data by B. A. Malyarchuk

“…It was shown that the formation of the modern appearance of the Russian mitochondrial gene pool began approximately 4 thousand years B.C. due to the influx of mtDNA haplotypes characteristic of the population of Central and Western Europe to the east of Europe. …”
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Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host. by Martine Bangratz, Aurore Comte, Estelle Billard, Abdoul Kader Guigma, Guillaume Gandolfi, Abalo Itolou Kassankogno, Drissa Sérémé, Nils Poulicard, Charlotte Tollenaere

“…The method described thus allows to identify various haplotypes of RYMV simultaneously infecting a single rice plant, obtaining their full-length sequences, as well as a rough estimate of relative frequencies within the sample. …”
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The role of Anatolia between Asia and Europe: A case study of oak gall wasp species, Cynips quercus (Hymenoptera, Cynipidae) by Serdar Dinç, Serap Mutun

“…Phylogenetic analysis grouped the Turkish haplotypes with the Iranian sequences, and Spain was grouped with Hungary. …”
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Discovery and Evaluation of Polymorphisms in the and Promoter Regions for Risk of Korean Lung Cancer by Jae Sook Sung, Kyong Hwa Park, Seung Tae Kim, Yeul Hong Kim

“…Statistical analyses revealed that the genotypes and haplotypes in the AKT2 and AKT3 promoter regions were not significantly associated with the risk of lung cancer in the Korean population. …”
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Neolithic introgression of IL23R-related protection against chronic inflammatory bowel diseases in modern EuropeansResearch in context by Ben Krause-Kyora, Nicolas Antonio da Silva, Elif Kaplan, Daniel Kolbe, Inken Wohlers, Hauke Busch, David Ellinghaus, Amke Caliebe, Efe Sezgin, Almut Nebel, Stefan Schreiber, Sabine Schade-Lindig, Joachim Wahl, Carola Berszin, Michael Francken, Irina Görner, Kerstin Schierhold, Joachim Pechtl, Gisela Grupe, Johannes Müller

“…In these samples, the investigation focused on admixture-informed analyses and selection scans of rs11209026-A and its haplotypes. Findings: rs11209026-A was found at high frequencies in Anatolian Farmers (AF, 18%). …”
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Spatial Distribution of Genetic, Ploidy, and Morphological Variation of the Edaphic Steno-Endemic <i>Alyssum moellendorfianum</i> (Brassicaceae) from the Western Balkans by Jasna Hanjalić Kurtović, Belma Kalamujić Stroil, Sonja Siljak-Yakovlev, Naris Pojskić, Adaleta Durmić-Pašić, Alma Hajrudinović-Bogunić, Lejla Lasić, Lejla Ušanović, Faruk Bogunić

“…Clear divergence between diploids and tetraploids was shown by AFLP, while plastid DNA sequences confirmed private haplotypes in each of the studied populations. Higher genetic diversity and allelic richness following the north-south pattern were documented in tetraploids compared to diploids, as indicated by nuclear microsatellites. …”
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Modeling dynamic changes in type 1 diabetes progression:Quantifying $\beta$-cell variation after the appearance ofislet-specific autoimmune responses by Patrick Nelson, Noah Smith, Stanca Ciupe, Weiping Zou, Gilbert S. Omenn, Massimo Pietropaolo

“…The model assumes that all individuals carryingsusceptible HLA haplotypes will develop variable degrees of T1DM-related immunologic abnormalities. …”
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Genetic diversity of the Aporrectodea caliginosa complex in Russia by S. V. Shekhovtsov, E. V. Golovanova, N. E. Bazarova, Yu. N. Belova, D. I. Berman, E. A. Derzhinsky, M. P. Shashkov, S. E. Peltek

“…A subset of individuals with pigmentation characteristic of A. c. caliginosa contained cox1 haplotypes of A. c. trapezoides; analysis of nuclear gene sequences confirmed this diagnosis. …”
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Molecular genetics of idiopathic pulmonary fibrosis by R. N. Mustafin

“…Genetic studies have shown a role of mutations and polymorphisms in mucin genes (MUC5B), in the genes responsible for the integrity of telomeres (TERC, TERC, TINF2, DKC1, RTEL1, PARN), in surfactant-related genes (SFTPC, SFTPCA, SFTPA2, ABCA3, SP-A2), immune system genes (IL1RN, TOLLIP), and haplotypes of HLA genes (DRB1*15:01, DQB1*06:02) in IPF pathogenesis. …”
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Comparisons of CVID and IgGSD: Referring Physicians, Autoimmune Conditions, Pneumovax Reactivity, Immunoglobulin Levels, Blood Lymphocyte Subsets, and HLA-A and -B Typing in 432 Ad... by James C. Barton, Luigi F. Bertoli, J. Clayborn Barton

“…Similarities included specialties of referring physicians, mean ages, proportions of women, reactivity to Pneumovax, median serum IgG3 and IgG4 levels, median blood CD56+/CD16+ lymphocyte levels, positivity for HLA-A and -B types, and frequencies of selected HLA-A, -B haplotypes. Dissimilarities included greater prevalence of autoimmune conditions, lower median IgG, IgA, and IgM, and lower median CD19+, CD3+/CD4+, and CD3+/CD8+ blood lymphocytes in CVID patients. …”
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Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds by N. S. Yudin, A. A. Yurchenko, D. M. Larkin

“…Signatures of selection, such as specific changes in the frequency of alleles and haplotypes, as well as the reduction or increase in genetic diversity, help to identify changes in the cattle genome in response to natural and artificial selection, as well as loci and genetic variants directly affecting adaptive and economically important traits. …”
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Structure and origin of Tuvan gene pool according to autosome SNP and Y-chromosome haplogroups by V. A. Stepanov, N. A. Kolesnikov, L. V. Valikhova, A. A. Zarubin, I. Yu. Khitrinskaya, V. N. Kharkov

“…The results of the analysis of the frequencies of autosomal SNPs by various methods, the similarities in the composition of the Y-chromosome haplogroups and YSTR haplotypes show that the gene pool of the Tuvans is very heterogeneous in terms of the composition of genetic components. …”
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