Article
Biotechnology & Applied Microbiology
Young-Lim Lee, Mirte Bosse, Haruko Takeda, Gabriel Costa Monteiro Moreira, Latifa Karim, Tom Druet, Claire Oget-Ebrad, Wouter Coppieters, Roel F. Veerkamp, Martien A. M. Groenen, Michel Georges, Aniek C. Bouwman, Carole Charlier
Summary: This study aimed to generate and explore a high-quality bovine structural variant (SV) catalogue and discovered two high impact duplications affecting gene expression. These duplications are associated with postpartum feed intake and hoof health traits. However, most copy number variants (CNVs) were not captured by the 50K genotyping array.
Article
Biochemistry & Molecular Biology
Brian M. Schilder, Towfique Raj
Summary: This study identified likely causal variants associated with Parkinson's disease susceptibility through fine-mapping methods and integrated epigenomic profiles to reveal the potential mechanism of action of these variants. The comprehensive list provided by this study may serve as targets in the development of more effective Parkinson's therapeutics.
HUMAN MOLECULAR GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Antonela Blazekovic, Kristina Gotovacjercic, Fran Borovecki
Summary: The study aimed to assess differences in 3'UTR variants of the SNCA gene in a cohort of PD patients and control subjects from Croatia, identifying a significantly higher occurrence of a particular variant in the PD population which has not been reported previously. Further research is needed to explore the role of these variants in PD development and their impact on disease pathology.
Article
Multidisciplinary Sciences
Vivian Link, Yuomi Jhony A. Zavaleta, Rochelle-Jan Reyes, Linda Ding, Judy Wang, Rori V. Rohlfs, Michael D. Edge
Summary: The 20 short tandem repeat (STR) loci of the combined DNA index system (CODIS) are widely used in forensic genetics in the United States. Although CODIS loci were previously believed to contain limited information about ancestry or traits, recent research has shown that the regions surrounding CODIS loci are enriched with trait-related variants.
Article
Biotechnology & Applied Microbiology
Johannes Geibel, Nora Paulina Praefke, Steffen Weigend, Henner Simianer, Christian Reimer
Summary: This study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate the linkage disequilibrium (LD) patterns between the called SVs and surrounding SNPs. The results indicated that LD between deletions (DELs) and SNPs was similar to LD between SNPs, while LD between other SVs and SNPs was significantly reduced. The main reason for the reduced LD was the presence of local minor allele frequency differences. Genotyping accuracy was lower for duplications (DUP), inversions (INV), and translocation breakpoints (BND) compared to SNPs and deletions (DELs). The presence of tag SNPs was slightly lower for DELs compared to WGS SNPs, but this difference disappeared when considering SNPs located on different chicken genotyping arrays.
Review
Agronomy
Theo Meuwissen, Ben Hayes, Iona MacLeod, Michael Goddard
Summary: This review discusses the possibility of identifying causal variants for complex traits, stressing the importance of large and diverse samples, accurate genotypes, multiple phenotypes, annotation of genomic sites, and other types of evidence required for this task.
Article
Clinical Neurology
Alexander M. Kulminski, Ian Philipp, Yury Loika, Liang He, Irina Culminskaya
Summary: The protective role of the apolipoprotein E (APOE) epsilon 2 allele in Alzheimer's disease (AD) may be influenced by different immunomodulation functions of TOMM40 and APOE variants in a sex-specific manner, defining a more homogeneous AD-protective epsilon 2/epsilon 3-bearing profile in men.
ALZHEIMERS & DEMENTIA
(2021)
Article
Cell Biology
Alexander M. Kulminski, Ethan Jain-Washburn, Ian Philipp, Liang He, Yury Loika, Elena Loiko, Olivia Bagley, Svetlana Ukraintseva, Anatoliy Yashin, Konstantin Arbeev, Eric Stallard, Mary F. Feitosa, Nicole Schupf, Kaare Christensen, Irina Culminskaya
Summary: Age-related diseases are complex polygenic traits with intricate genetic architectures. We examined the impact of multiple combinations of genotypes on the chances of living to older ages and found that specific combinations of genetic variants were associated with increased risk for Alzheimer's disease and decreased survival chances.
Article
Biochemistry & Molecular Biology
Krystyna Nadachowska-Brzyska, Ludovic Dutoit, Linnea Smeds, Martin Kardos, Lars Gustafsson, Hans Ellegren
Summary: Long-term effective population size (N-e) is crucial in evolutionary biology and population genetics, with numerous estimates available for various species and populations. However, estimating contemporary N-e remains challenging, especially with LD-based methods. Whole-genome sequencing data offers new possibilities in estimating high contemporary N-e.
Article
Oncology
Juan A. Santamaria-Barria, Chikako Matsuba, Adam Khader, Anthony J. Scholar, Mary Garland-Kledzik, Trevan D. Fischer, Richard Essner, Matthew P. Salomon, Joshua M. V. Mammen, Melanie Goldfarb
Summary: This study analyzed melanoma samples and identified age-related mutational differences, as well as potential targetable mutations for personalized therapies.
JOURNAL OF SURGICAL ONCOLOGY
(2023)
Article
Geriatrics & Gerontology
Alexander M. Kulminski, Ian Philipp, Leonardo Shu, Irina Culminskaya
Summary: This study explores the roles of genetic variants in the APOE-TOMM40-APOC1 region in Alzheimer's disease risk, showing that carriers of certain alleles have significantly higher risk for AD.
NEUROBIOLOGY OF AGING
(2022)
Article
Biochemical Research Methods
Jingfen Lan, Wenxiang Chen, Ganggang Yin, A. K. Alvi Haque, Kun Xie, Qiang Yu, Xiguo Yuan
Summary: Single nucleotide variants (SNVs) are common in human genome and have significant effects on tumor development and genetic diseases. LDSSNV is a new method that can detect and distinguish between somatic and germline SNVs. It shows great potential in tumor genome analysis.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Karim Karimi, Duy Ngoc Do, Mehdi Sargolzaei, Younes Miar
Summary: The study demonstrates the importance of understanding the genetic structure of American mink for the development of genomic breeding strategies. Significant genetic variation was observed among color-types, with admixture analysis suggesting three ancestral populations as the most suitable. The density of 120,000 and 24,000 SNPs was identified as adequate for genomic evaluation accuracy in CCFAR and Millbank Fur Farm populations, respectively.
Review
Biochemical Research Methods
Tingting Gong, Vanessa M. Hayes, Eva K. F. Chan
Summary: This review highlights important factors affecting somatic SV detection and compares the performance of seven commonly used SV callers. By focusing on changes in sensitivity and precision for detecting different SV types and size ranges from samples with varying variant allele frequencies and sequencing depths, the evaluation findings extend beyond the seven SV callers examined in this paper.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Haoqiang Ye, Zipeng Zhang, Duanyang Ren, Xiaodian Cai, Qianghui Zhu, Xiangdong Ding, Hao Zhang, Zhe Zhang, Jiaqi Li
Summary: The size of reference population is important for genomic prediction. This study used WGS data to construct LD-based haplotypes and explored the impact of different SNP densities, variant representation, and reference population size on prediction accuracy. The results showed that GBLUP using WGS data improved prediction accuracy in multi-population and haplotype method had better performance in multi-population genomic evaluation.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Clare Horscroft, Sarah Ennis, Reuben J. Pengelly, Timothy J. Sluckin, Andrew Collins
BRIEFINGS IN BIOINFORMATICS
(2019)
Article
Biochemical Research Methods
Reuben J. Pengelly, Andrew Collins
Review
Biotechnology & Applied Microbiology
Dareen Alyousfi, Diana Baralle, Andrew Collins
BRIEFINGS IN FUNCTIONAL GENOMICS
(2019)
Article
Multidisciplinary Sciences
Wai Yee Low, Rick Tearle, Derek M. Bickhart, Benjamin D. Rosen, Sarah B. Kingan, Thomas Swale, Francoise Thibaud-Nissen, Terence D. Murphy, Rachel Young, Lucas Lefevre, David A. Hume, Andrew Collins, Paolo Ajmone-Marsan, Timothy P. L. Smith, John L. Williams
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Alejandra Vergara-Lope, Sarah Ennis, Igor Vorechovsky, Reuben J. Pengelly, Andrew Collins
EUROPEAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Ecology
M. Reza Jabalameli, Clare Horscroft, Alejandra Vergara-Lope, Reuben J. Pengelly, Andrew Collins
Article
Multidisciplinary Sciences
Alejandra Vergara-Lope, M. Reza Jabalameli, Clare Horscroft, Sarah Ennis, Andrew Collins, Reuben J. Pengelly
Article
Oncology
Stuart J. Blakemore, Ruth Clifford, Helen Parker, Pavlos Antoniou, Ewa Stec-Dziedzic, Marta Larrayoz, Zadie Davis, Latha Kadalyayil, Andrew Colins, Pauline Robbe, Dimitris Vavoulis, Jade Forster, Louise Carr, Ricardo Morilla, Monica Else, Dean Bryant, Helen McCarthy, Renata J. Walewska, Andrew J. Steele, Jacqueline Chan, Graham Speight, Tanja Stankovic, Mark S. Cragg, Daniel Catovsky, David G. Oscier, Matthew J. J. Rose-Zerilli, Anna Schuh, Jonathan C. Strefford
Review
Biochemical Research Methods
Dareen Alyousfi, Diana Baralle, Andrew Collins
Summary: More than 50% of causal genetic variants underlying potential single gene disorders remain undiscovered, affecting clinical management without confirmed molecular diagnoses. The ESPP score has been developed to aid in filtering genome sequence data and identify genes with high potential for pathogenic disease-related variation. Recognizing gene essentiality can guide the identification of causal variants and improve genome sequence filtering.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Dentistry, Oral Surgery & Medicine
Alejandro Silva Espinosa, Julio Cesar Martinez, Yubahhaline Molina, Maria Alejandra Bermudez Gordillo, Daniel Ramos Hernandez, Daniela Zarate Rivera, Blanka Pacheco Olmos, Nathaly Ramirez, Liliana Arias, Andres Zarate, Q. Diana Marcela Diaz, Andrew Collins, Alvaro Mauricio Herrera Cepeda, Ignacio Briceno Balcazar
Summary: The study found that left cleft lip and palate and nonsyndromic forms were the most common types in the population, with the most frequent comorbidities being psychomotor retardation and heart disease. A low proportion of mothers were exposed to passive smoking during pregnancy, while low birth weight accounted for a significant number of cases.
CLEFT PALATE CRANIOFACIAL JOURNAL
(2022)
Article
Gastroenterology & Hepatology
Shreya Sharma, William J. Tapper, Andrew Collins, Zaed Z. R. Hamady
Summary: The study found that PDAC is associated with DM, particularly with NODM. The developed PRS models show good performance in identifying PDAC patients with NODM and long-standing DM, and can improve clinical risk assessment models.
Article
Genetics & Heredity
Daniel Uricoechea Patino, Andrew Collins, Oscar Julian Romero Garcia, Gustavo Santos Vecino, Jose Vicente Rodriguez Cuenca, Jaime E. Bernal, Escilda Benavides Benitez, Saray Vergara Munoz, Ignacio Briceno Balcazar
Summary: Analysis of mitochondrial DNA data from ancient human remains reveals high population heterogeneity among pre-Hispanic populations in Colombia.
Article
Hematology
Tomasz K. Wojdacz, Harindra E. Amarasinghe, Latha Kadalayil, Alice Beattie, Jade Forster, Stuart J. Blakemore, Helen Parker, Dean Bryant, Marta Larrayoz, Ruth Clifford, Pauline Robbe, Zadie A. Davis, Monica Else, Dena R. Howard, Basile Stamatopoulos, Andrew J. Steele, Richard Rosenquist, Andrew Collins, Andrew R. Pettitt, Peter Hillmen, Christoph Plass, Anna Schuh, Daniel Catovsky, David G. Oscier, Matthew J. J. Rose-Zerilli, Christopher C. Oakes, Jonathan C. Strefford
Article
Biochemical Research Methods
Reuben J. Pengelly, Alejandra Vergara-Lope, Dareen Alyousfi, M. Reza Jabalameli, Andrew Collins
BRIEFINGS IN BIOINFORMATICS
(2019)
Meeting Abstract
Hematology
S. S. Sahota, W. Tapper, N. J. Weston-Bell, A. Bolomsky, A. R. Collins, N. Zojer, D. Bryant