Article
Biochemistry & Molecular Biology
Daniel P. Cooke, David C. Wedge, Gerton Lunter
Summary: Genotyping from sequencing is essential in the molecular breeding of polyploid plants. We evaluated Octopus and other tools on polyploid data sets and found that Octopus has fewer errors in genotyping compared to other methods.
Article
Biochemistry & Molecular Biology
David Gerard
Summary: The study focuses on the estimation of linkage disequilibrium (LD) in polyploids, characterizing haplotypic and composite measures of LD and deriving estimation procedures with genotype uncertainty. The methods directly estimate LD from genotype likelihoods and provide standard errors for all LD estimators discussed, validated on both real and simulated data.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
Joyce N. Njuguna, Lindsay V. Clark, Alexander E. Lipka, Kossonou G. Anzoua, Larisa Bagmet, Pavel Chebukin, Maria S. Dwiyanti, Elena Dzyubenko, Nicolay Dzyubenko, Bimal Kumar Ghimire, Xiaoli Jin, Douglas A. Johnson, Jens Bonderup Kjeldsen, Hironori Nagano, Ivone de Bem Oliveira, Junhua Peng, Karen Koefoed Petersen, Andrey Sabitov, Eun Soo Seong, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Patricio Munoz, Stephen P. Long, Erik J. Sacks
Summary: Discovery and analysis of genetic variants underlying agriculturally important traits are crucial for molecular breeding of crops. Accurate genotype calling from next-generation sequencing data is challenging in polyploid species. Bayesian statistical methods can accurately estimate allelic dosage in any ploidy. Continuous genotypes can improve the accuracy of genomic prediction.
Article
Biology
Jesse Farek, Daniel Hughes, William Salerno, Yiming Zhu, Aishwarya Pisupati, Adam Mansfield, Olga Krasheninina, Adam C. English, Ginger Metcalf, Eric Boerwinkle, Donna M. Muzny, Richard Gibbs, Ziad Khan, Fritz J. Sedlazeck
Summary: xAtlas is a fast, lightweight, and accurate method for calling SNVs and small indels, with rapid runtimes, support for various file formats, and retraining capabilities.
Review
Biochemistry & Molecular Biology
Monica Valecha, David Posada
Summary: Single-cell sequencing data is error-prone due to technical biases, and there are various methods for single-cell variant calling that often result in many discordant calls when applied to real data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Infectious Diseases
Linda Grillova, Thomas Cokelaer, Jean-Francois Mariet, Juliana Pipoli da Fonseca, Mathieu Picardeau
Summary: By using hybridization capture followed by Illumina sequencing, we were able to determine the genetic diversity of circulating Leptospira strains in mainland France. The capture had a significant increase in pathogen reads and allowed us to confidently identify the infecting strains. This method provides new opportunities for understanding the epidemiology and pathogenesis of this fastidious pathogen.
BMC INFECTIOUS DISEASES
(2023)
Article
Multidisciplinary Sciences
Katherine D. Arias, Isabel Alvarez, Juan Pablo Gutierrez, Ivan Fernandez, Juan Menendez, Nuria A. Menendez-Arias, Felix Goyache
Summary: This study genotyped Gochu Asturcelta pig parents-offspring trios to identify the causes of Mendelian errors (ME). The majority of ME were caused by systematic factors, and these errors may have an impact on genotyping quality and genetic research outcomes.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
August E. Woerner, Sammed Mandape, Kapema Bupe Kapema, Tiffany M. Duque, Amy Smuts, Jonathan L. King, Benjamin Crysup, Xuewen Wang, Meng Huang, Jianye Ge, Bruce Budowle
Summary: One of the goals of forensic genetics is to determine the attribution of a sample, whether it is associated with a person or persons. Whole genome techniques, which sample the entirety or a large portion of the genome, may provide better relationship determinations compared to limited locus sampling. However, these techniques are still relatively new in the field of forensic sciences. Bioinformatic pipelines, using approaches from medical and population genomic literature, are introduced for estimating kinship using whole genome sequencing. Different variant callers are considered and two specific pipelines are evaluated. Filters and thresholds are optimized for the purpose of estimating kinship. With appropriate filtering and thresholds, both tools perform similarly, with DeepVariant producing more accurate genotypes but slightly less accurate overall estimates of relatedness.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
Article
Genetics & Heredity
Davide Bolognini, Alberto Magi
Summary: This research evaluates the performance of five long-read SV callers across four long-read aligners using both real and synthetic nanopore datasets. It focuses on the effects of read alignment, sequencing coverage, and variant allele depth on the detection and genotyping of SVs of different types and size ranges. Insights into precision and recall of SV callsets generated by integrating various long-read aligners and SV callers are provided.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Juanita Gil, Juan Sebastian Andrade-Martinez, Jorge Duitama
Summary: TILLING is a powerful reverse genetics method used in plant functional genomics and breeding to identify mutagenized individuals with improved behavior for a trait of interest. However, the main issue lies in the fact that current bioinformatics tools are not designed to detect low frequency mutations in pooled samples or assign variants detected in overlapping pools to individual samples.
FRONTIERS IN GENETICS
(2021)
Article
Pharmacology & Pharmacy
Shishi Luo, Ruomu Jiang, Joseph J. Grzymski, William Lee, James T. Lu, Nicole L. Washington
Summary: Genomic-guided pharmaceutical prescribing is increasingly important, and accurate genotyping of pharmacogenomic genes can be challenging due to their complex genetic architecture. The Helix PGx database provides frequency data for CYP2C9, CYP2C19, CYP2D6, and CYP4F2, demonstrating high diversity in CYP2D6 and higher frequency of rare alleles in non-European populations. Most individuals in the cohort carry high-risk variants in pharmacogenes, suggesting that screening these genes could impact a significant portion of the general population.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2021)
Article
Nutrition & Dietetics
Jacus S. Nacis, Jason Paolo H. Labrador, Diana Glades D. Ronquillo, Marietta P. Rodriguez, Aurora Maria Francesca D. Dablo, Ruby D. Frane, Marilou L. Madrid, Noelle Lyn C. Santos, Julianne Janine V. Carrillo, Mikko Glen Fernandez, Gerard Bryan L. Gonzales
Summary: This study aims to investigate whether providing nutrition and lifestyle recommendations based on individual genotype can lead to weight loss and reduction in BMI, waist circumference, and body fat percentage among overweight and obese adults. The study will be a randomized controlled trial, with participants randomly allocated to either the intervention or control group. The study will contribute to the future implementation of precision nutrition interventions by providing evidence on the effectiveness of gene-based nutrition and lifestyle recommendations for weight loss.
FRONTIERS IN NUTRITION
(2023)
Article
Multidisciplinary Sciences
Ewa Sieliwonczyk, Bert Vandendriessche, Charlotte Claes, Evy Mayeur, Maaike Alaerts, Philip Holmgren, Tycho Canter Cremers, Dirk Snyders, Bart Loeys, Dorien Schepers
Summary: Despite challenges, researchers have developed a novel method to improve knock-in efficiency using CRISPR-Cas9 technique in zebrafish. By combining the early selection procedure with genotyping and next-generation sequencing, they achieved a significant increase in somatic editing efficiency and demonstrated potential for improving germline transmission in pre-selected embryos.
SCIENTIFIC REPORTS
(2023)
Article
Pharmacology & Pharmacy
David Twesigomwe, Britt I. Drogemoller, Galen E. B. Wright, Azra Siddiqui, Jorge da Rocha, Zane Lombard, Scott Hazelhurst
Summary: StellarPGx is a Nextflow pipeline for accurately genotyping CYP genes by combining genome graph-based variant detection and read coverage information. It demonstrated high accuracy and reliability in genotyping CYP genes, especially in complex cases like CYP2D6. The pipeline is open-source and available, showcasing its potential for research and clinical pharmacogenomics applications.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2021)
Article
Genetics & Heredity
Kaat Rubben, Laurentijn Tilleman, Koen Deserranno, Olivier Tytgat, Dieter Deforce, Filip Van Nieuwerburgh
Summary: CYP2D6 is a crucial pharmacogene responsible for metabolizing or activating a significant portion of clinically used drugs. However, genotyping this gene is challenging due to its high similarity with neighboring pseudogenes and frequent formation of CYP2D6-CYP2D7 hybrids. In this study, a genotyping assay was developed using the nCATS-CoLoRGen pipeline, which accurately determines the complete sequence of CYP2D6-CYP2D7 and improves gene function prediction.
Article
Agronomy
Wang Shuhang, Roeland E. Voorrips, Greet Steenhuis-Broers, Ben Vosman, Joop J. A. van Loon
Article
Agronomy
Roeland E. Voorrips, Marco C. A. M. Bink, Johannes W. Kruisselbrink, Herma J. J. Koehorst-van Putten, W. Eric van de Weg
MOLECULAR BREEDING
(2016)
Article
Agronomy
Giorgio Tumino, Roeland E. Voorrips, Fulvia Rizza, Franz W. Badeck, Caterina Morcia, Roberta Ghizzoni, Christoph U. Germeier, Maria-Joao Paulo, Valeria Terzi, Marinus J. M. Smulders
THEORETICAL AND APPLIED GENETICS
(2016)
Article
Genetics & Heredity
Chaozhi Zheng, Roeland E. Voorrips, Johannes Jansen, Christine A. Hackett, Julie Ho, Marco C. A. M. Bink
Article
Multidisciplinary Sciences
Konrad Zych, Basten L. Snoek, Mark Elvin, Miriam Rodriguez, K. Joeri Van der Velde, Danny Arends, Harm-Jan Westra, Morris A. Swertz, Gino Poulin, Jan E. Kammenga, Rainer Breitling, Ritsert C. Jansen, Yang Li
Article
Ecology
Awang Maharijaya, Ben Vosman, Koen Pelgrom, Yuni Wahyuni, Ric C. H. de Vos, Roeland E. Voorrips
ARTHROPOD-PLANT INTERACTIONS
(2019)
Article
Biochemistry & Molecular Biology
Jakob Wirbel, Paul Theodor Pyl, Ece Kartal, Konrad Zych, Alireza Kashani, Alessio Milanese, Jonas S. Fleck, Anita Y. Voigt, Albert Palleja, Ruby Ponnudurai, Shinichi Sunagawa, Luis Pedro Coelho, Petra Schrotz-King, Emily Vogtmann, Nina Habermann, Emma Nimeus, Andrew M. Thomas, Paolo Manghi, Sara Gandini, Davide Serrano, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Levi Waldron, Alessio Naccarati, Nicola Segata, Rashmi Sinha, Cornelia M. Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller
Article
Genetics & Heredity
Peter M. Bourke, Christine A. Hackett, Roeland E. Voorrips, Richard G. F. Visser, Chris Maliepaard
G3-GENES GENOMES GENETICS
(2019)
Article
Biochemical Research Methods
Peter M. Bourke, Roeland E. Voorrips, Christine A. Hackett, Geert van Geest, Johan H. Willemsen, Paul Arens, Marinus J. M. Smulders, Richard G. F. Visser, Chris Maliepaard
Summary: polyqtlR is a software tool designed for polyploid crops, allowing QTL interval mapping in populations of any ploidy level using identity-by-descent probabilities. It enables exploration of allelic composition of discovered QTL and includes visualization tools, as well as options to analyze polyploid meiosis processes.
Article
Biochemical Research Methods
Roeland E. Voorrips, Giorgio Tumino
Summary: This study presents a new method to reconstruct haplotypes from SNP dosages derived from genotyping arrays in polyploids. The method shows higher accuracy compared to existing software, especially in the presence of full-sib families. The results demonstrate the usefulness of this method in polyploid genetic analysis.
BMC BIOINFORMATICS
(2022)
Article
Agronomy
Jorge Aleman-Baez, Jian Qin, Chengcheng Cai, Chunmei Zou, Johan Bucher, Maria-Joao Paulo, Roeland E. Voorrips, Guusje Bonnema
Summary: Correlations between the morphological traits of cabbage rosette leaves and heads were identified, and 50 robust quantitative trait loci (QTLs) were found through genome-wide association studies. Half of these loci affect both organs. This study provides valuable insights into the relationship and genetic basis of leaf development and leafy head formation in cabbage.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Biology
Francesco Del Carratore, Konrad Zych, Matthew Cummings, Eriko Takano, Marnix H. Medema, Rainer Breitling
COMMUNICATIONS BIOLOGY
(2019)
Correction
Genetics & Heredity
P. M. Bourke, R. E. Voorrips, R. G. F. Visser, C. Maliepaard