Article
Biochemical Research Methods
Michael Schneider, Asis Shrestha, Agim Ballvora, Jens Leon
Summary: The proposed strategy accurately identifies the allele frequency of populations at low cost. This is particularly important for evolutionary plant breeding of crops with large genomes, such as barley. Whole-genome low coverage re-sequencing at 0.03x coverage per genotype accurately estimates allele frequency when a loci-based haplotyping approach is applied. The implementation of annotated haplotypes capitalizes on the biological background and statistical robustness.
Article
Immunology
Ute V. Solloch, Anette S. Giani, Maria Ignacia Pattillo Garnham, Juergen Sauter, Stefanie N. Bernas, Vinzenz Lange, Francisco Barriga, Marcelo A. Fernandez-Vina, Alexander H. Schmidt
Summary: Hematopoietic stem cell transplantation often requires unrelated stem cell donors matched in HLA genes. The extensive allelic variability of the HLA system complicates donor search, hence the need for large registries. This study analyzed HLA allele and haplotype frequencies of DKMS Chile donors, identifying alleles more abundant in the Chilean subpopulations, particularly in the Mapuche. The study also revealed limited benefits for Chilean patients from non-Chilean donor registries, emphasizing the need for ongoing donor recruitment efforts in Chile.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemical Research Methods
Thomas A. Delomas, Stuart C. Willis
Summary: New methods have been developed for estimating microhaplotype allele frequency from low-coverage whole genome sequencing and pooled sequencing data, which have been validated using datasets from three non-model organisms. These methods will allow the design of microhaplotype panels and the discovery and evaluation of candidate loci using low-coverage WGS and pool-seq data.
BMC BIOINFORMATICS
(2023)
Review
Health Care Sciences & Services
Tatyana E. Lazareva, Yury A. Barbitoff, Anton I. Changalidis, Alexander A. Tkachenko, Evgeniia M. Maksiutenko, Yulia A. Nasykhova, Andrey S. Glotov
Summary: With the advancements in collection, storage, and analysis of biological samples, many countries have established large biobanks, which play a significant role in medical genetics and genomic research. They provide reference allele frequency information and enable large-scale cross-ancestry meta-analyses. Biobanks are extensively used in genomics for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Andrew Webb, Jared Knoblauch, Nitesh Sabankar, Apeksha Sukesh Kallur, Jody Hey, Arun Sethuraman
Summary: The Pop-Gen Pipeline Platform (PPP) is an open-source software platform designed for population genomic analyses in a consistent and standardized Python environment. The platform encompasses entire workflows for input preparation, file format conversion, various population genomic analyses, and output generation, with reproducibility and extensibility in mind. Users can download and use PPP at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Immunology
N. Sacchi, F. Ciceri, F. Bonifazi, M. Algeri, A. Gallina, S. Pollichieni, E. Raggio, B. Hadj-Amar, L. Lombardini, S. Pupella, G. Liumbruno, M. Cardillo
Summary: In Italy, the primary donor for allogeneic hematopoietic stem cell transplantation is currently an HLA-matched unrelated donor when a matched sibling is not found. The study suggests that recruiting over 2 million donors is needed to increase the likelihood of finding an 8/8 HLA-matched donor for 50% of Italian patients, and the probability of finding a 7/8 HLA-matched donor significantly increases if accepting one mismatch at HLA I class loci. Additionally, the probability of recruiting a donor with a new HLA phenotype in different Italian regions was also calculated based on regional haplotype frequencies.
Article
Biochemistry & Molecular Biology
Tzahi Gabzi, Yitzhak Pilpel, Tamar Friedlander
Summary: This article investigates the fitness landscape of a yeast tRNA gene and finds that the wild type allele is sub-optimal. It also rules out the possibility that the wild type is the fittest on average or located on a local fitness maximum under four different conditions. The study further reveals that the wild type is mutationally robust, while more fit variants are typically mutationally fragile. Similar observations have been made in viral genomes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Oncology
Craig M. Bielski, Barry S. Taylor
Summary: The search for somatic mutations that drive human tumors has been a focus in recent cancer research, with less emphasis on understanding the serial genetic evolution of driver mutations. Changes in mutant oncogene zygosity are common and can lead to selective growth advantages. Further research is needed to fully understand the implications of mutant allele imbalance in tumor biology, cancer evolution, and response to anticancer therapy.
ANNUAL REVIEW OF CANCER BIOLOGY, VOL 5, 2021
(2021)
Article
Biochemistry & Molecular Biology
Jeremy D. Lange, Heloise Bastide, Justin B. Lack, John E. Pool
Summary: Population genetics aims to understand the forces shaping genetic variation by analyzing snapshots of genomic variation. Utilizing multiple sampling times to study changes in allele frequencies can help clarify the roles of neutral and non-neutral forces on short time scales. This study compares the genome sequence variations of Drosophila melanogaster samples collected at different time points and reveals a relatively small local effective population size and non-neutral variations in certain genes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Nozomi Uemura, Shogo Furutani, Takashi Tomita, Kentaro Itokawa, Osamu Komagata, Shinji Kasai
Summary: This study aimed to evaluate the viability of Ae. aegypti with concomitant L982W + F1534C mutations in Vgsc. The researchers crossed a resistant strain with a susceptible strain for 15 generations and found that the proportion of wild-type homozygotes increased, indicating a fitness cost of these mutations. The allele frequencies of L982W + F1534C showed a decreasing trend over generations, suggesting potential recovery of pyrethroid susceptibility over time.
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
(2023)
Article
Biochemical Research Methods
Xinping Fan, Guanghao Luo, Yu S. Huang
Summary: This study presents Accucopy, a method for inferring total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity and low-coverage tumor samples. Accucopy utilizes robust statistical techniques and models such as the tiered Gaussian mixture model, expectation-maximization algorithm, and sparse Bayesian learning, outperforming other methods in simulated and real sequencing samples.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Elzbieta Kaja, Adrian Lejman, Dawid Sielski, Mateusz Sypniewski, Tomasz Gambin, Mateusz Dawidziuk, Tomasz Suchocki, Pawel Golik, Marzena Wojtaszewska, Magdalena Mroczek, Maria Stepien, Joanna Szyda, Karolina Lisiak-Teodorczyk, Filip Wolbach, Daria Kolodziejska, Katarzyna Ferdyn, Maciej Dabrowski, Alicja Wozna, Marcin Zytkiewicz, Anna Bodora-Troinska, Waldemar Elikowski, Zbigniew J. Krol, Artur Zaczynski, Agnieszka Pawlak, Robert Gil, Waldemar Wierzba, Paula Dobosz, Katarzyna Zawadzka, Pawel Zawadzki, Pawel Sztromwasser
Summary: Despite Slavic populations accounting for over 4.5% of the world's population, there is currently no centralized, open-source genetic variation reference database for any Slavic population. This study analyzed the whole genomes of 1222 Poles to identify and genotype various genomic variations. The results provide important genetic reference data for the Polish population and contribute to the worldwide genomic resources available to researchers and clinicians.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Jacqueline L. Gill, Jessica Hedge, Daniel J. Wilson, R. Craig MacLean
Summary: Our research shows that the MRSA strain Staphylococcus aureus ST239 originated from a large-scale recombination between ST8 and ST30 before 1945. Despite being primarily influenced by purifying selection, ST239 has undergone parallel evolution in genes related to antibiotic resistance and virulence. However, ST239 exhibits lower competitive fitness compared to other strains of S. aureus, which may explain its rapid decline in prevalence worldwide.
Article
Clinical Neurology
Olaitan Okunoye, Oluwadamilola O. Ojo, Oladunni Abiodun, Sani Abubakar, Charles Achoru, Olaleye Adeniji, Osigwe Agabi, Uchechi Agulanna, Rufus Akinyemi, Mohammed Ali, Ifeyinwa Ani-Osheku, Ohwotemu Arigbodi, Abiodun Bello, Cyril Erameh, Temitope Farombi, Michael Fawale, Frank Imarhiagbe, Emmanuel Iwuozo, Morenikeji Komolafe, Paul Nwani, Ernest Nwazor, Yakub Nyandaiti, Yahaya Obiabo, Olanike Odeniyi, Francis Odiase, Francis Ojini, Gerald Onwuegbuzie, Godwin Osaigbovo, Nosakhare Osemwegie, Olajumoke Oshinaike, Folajimi Otubogun, Shyngle Oyakhire, Simon Ozomma, Sarah Samuel, Funmilola Taiwo, Kolawole Wahab, Yusuf Zubair, Dena Hernandez, Sara Bandres-Ciga, Cornelis Blauwendraat, Andrew Singleton, Henry Houlden, John Hardy, Mie Rizig, Njideka Okubadejo
Summary: This study aimed to determine the frequencies of MAPT haplotypes and their role as risk factors for PD and age at onset in Nigerians. The frequency of the H1 haplotype was similar in both PD patients and controls, while the H2 haplotype was present in a low percentage in both groups. Our findings support previous studies that report a low frequency of the MAPT H2 haplotype in black ancestry Africans.
PARKINSONISM & RELATED DISORDERS
(2023)
Article
Genetics & Heredity
Fernanda M. Garcia, Raquel S. R. Trabach, Victor S. Stange, Bruno Cancian, Alexia S. S. Zetum, Matheus C. Casotti, Flavia I. V. Errera, Elizeu F. de Carvalho, Debora D. Meira, Iuri D. Louro
Summary: This study found that the population of Espirito Santo, Brazil is genetically closer to the Italian population based on the analysis of STR markers on the X chromosome.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2024)
Article
Biochemistry & Molecular Biology
Odrade Nougue, Elodie Flaven, Roula Jabbour-Zahab, Nicolas O. Rode, Marie-Pierre Dubois, Thomas Lenormand
BIOCHEMICAL SYSTEMATICS AND ECOLOGY
(2015)
Article
Ecology
O. Nougue, N. O. Rode, R. Jabbour-Zahab, A. Segard, L. -M. Chevin, C. R. Haag, T. Lenormand
JOURNAL OF EVOLUTIONARY BIOLOGY
(2015)
Article
Ecology
N. O. Rode, P. Soroye, R. Kassen, H. D. Rundle
Article
Agronomy
Yan Holtz, Michel Bonnefoy, Veronique Viader, Morgane Ardisson, Nicolas O. Rode, Gerard Poux, Pierre Roumet, Veronique Marie-Jeanne, Vincent Ranwez, Sylvain Santoni, David Gouache, Jacques L. David
THEORETICAL AND APPLIED GENETICS
(2017)
Article
Genetics & Heredity
Pierre-Henri Clergeot, Nicolas O. Rode, Sylvain Glemin, Mikael Brandstrom Durling, Katarina Ihrmark, Ake Olson
Article
Parasitology
Eva J. P. Lievens, Nicolas O. Rode, Julie Landes, Adeline Segard, Roula Jabbour-Zahab, Yannis Michalakis, Thomas Lenormand
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2019)
Review
Biodiversity Conservation
Nicolas O. Rode, Arnaud Estoup, Denis Bourguet, Virginie Courtier-Orgogozo, Florence Debarre
CONSERVATION GENETICS
(2019)
Article
Ecology
C. Leauthaud, P. Hiernaux, W. Musila, L. Kergoat, G. Manuela, S. Duvail, J. Albergel, N. Rode
Article
Entomology
Laure Olazcuaga, Nicolas O. Rode, Julien Foucaud, Benoit Facon, Virginie Ravigne, Aurelien Ausset, Nicolas Lemenager, Anne Loiseau, Mathieu Gautier, Arnaud Estoup, Ruth A. Hufbauer
ENVIRONMENTAL ENTOMOLOGY
(2019)
Article
Ecology
Brian S. Mautz, Nicolas O. Rode, Russell Bonduriansky, Howard D. Rundle
JOURNAL OF ANIMAL ECOLOGY
(2019)
Article
Evolutionary Biology
Helene Freville, Pierre Roumet, Nicolas Olivier Rode, Aline Rocher, Muriel Latreille, Marie-Helene Muller, Jacques David
EVOLUTIONARY APPLICATIONS
(2019)
Article
Genetics & Heredity
Nicolas O. Rode, Virginie Courtier-Orgogozo, Florence Debarre
G3-GENES GENOMES GENETICS
(2020)
Article
Biology
Christopher S. Angell, Mathieu J. Oudin, Nicolas O. Rode, Brian S. Mautz, Russell Bonduriansky, Howard D. Rundle
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Evolutionary Biology
F. Debarre, N. O. Rode, L. Ugelvig