Article
Multidisciplinary Sciences
Barbara Sousa da Mota, Simone Rubinacci, Diana Ivette Cruz Davalos, Carlos Eduardo G. Amorim, Martin Sikora, Niels N. Johannsen, Marzena H. Szmyt, Piotr Wlodarczak, Anita Szczepanek, Marcin M. Przybyla, Hannes Schroeder, Morten E. Allentoft, Eske Willerslev, Anna-Sapfo Malaspinas, Olivier Delaneau
Summary: This study investigates the accuracy of imitating ancient DNA for genotyping and whether imputation introduces bias to downstream analyses. The authors re-sequence an ancient trio and downsample and impute a total of 43 ancient genomes, finding that ancient and modern DNA imputation accuracies are comparable.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Bruno Ariano, Valeria Mattiangeli, Emily M. Breslin, Eoin W. Parkinson, T. Rowan McLaughlin, Jess E. Thompson, Ronika K. Power, Jay T. Stock, Bernardette Mercieca-Spiteri, Simon Stoddart, Caroline Malone, Shyam Gopalakrishnan, Lara M. Cassidy, Daniel G. Bradley
Summary: This study explores the genetic characteristics of Late Neolithic human genomes from Malta, indicating maritime isolation and a distinct ancestry compared to mainland agricultural populations in Europe. The research also reveals the impact of Mediterranean expansion and island colonization on genetic geography during the Neolithic period.
Article
Biochemical Research Methods
Yilei Huang, Harald Ringbauer
Summary: This study presents a new method for estimating contamination in male modern human ancient DNA (aDNA). The method, called hapCon, outperforms existing approaches, especially in the low coverage regime. HapCon provides useful contamination estimates for very low coverage data and extends the coverage limit of previous methods. The study also demonstrates that hapCon has little bias for contamination up to a certain level and can be applied to aDNA from different time periods and global ancestries.
Article
Multidisciplinary Sciences
Eida Khalaf Almohammed, Abdullah Hadi, Maha Al-Asmakh, Hayder Lazim
Summary: The study analyzed the Y-STR genotypes of unrelated males from Qatar and found a predominance of haplogroup J1 in the Qatari population. The research also revealed the influence of Arabs on the indigenous Berbers of North Africa. Furthermore, the study explored the migration between Qatar and other Arabian populations. This study is important for understanding population genetic structure and ancestry.
Article
Multidisciplinary Sciences
Sam Tallman, Maria das Dores Sungo, Silvio Saranga, Sandra Beleza
Summary: This study presents a collection of 350 whole genome sequences from Angola and Mozambique, providing insights into significant demographic events in African history and shedding light on the complexity of the Bantu Expansion. The generated reference panels improve imputation accuracy in African Americans and Brazilians.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Tina Saupe, Francesco Montinaro, Cinzia Scaggion, Nicola Carrara, Toomas Kivisild, Eugenia D'Atanasio, Ruoyun Hui, Anu Solnik, Ophelie Lebrasseur, Greger Larson, Luca Alessandri, Ilenia Arienzo, Flavio De Angelis, Mario Federico Rolfo, Robin Skeates, Letizia Silvestri, Jessica Beckett, Sahra Talamo, Andrea Dolfini, Monica Miari, Mait Metspalu, Stefano Benazzi, Cristian Capelli, Luca Pagani, Christiana L. Scheib
Summary: The study uncovers the genetic evolution of individuals from the Chalcolithic and Bronze Age in central Italy, revealing the early appearance of Steppe-related ancestry as early as 1600 BCE with an increasing impact over time. Changes in burial patterns and genetic structure were observed, but did not directly lead to alterations in the frequencies of 115 phenotypes.
Article
Evolutionary Biology
Stuart C. Willis, Jon E. Hess, Jeff K. Fryer, John M. Whiteaker, Shawn R. Narum
Summary: Our study found that three major phylogeographic lineages of Chinook salmon in the Columbia River Basin share similar genetic variants in the chromosome 28 region, which are significantly associated with adult migration timing. Despite strong genetic differences in other genomic regions, the interior stream-type lineage exhibited genetic variations related to migration timing that were consistent with the other lineages. This indicates the potential for utilizing chromosome 28 variation to predict run timing in Chinook salmon populations.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Genetics & Heredity
Toomas Kivisild, Lehti Saag, Ruoyun Hui, Simone Andrea Biagini, Vasili Pankratov, Eugenia D'Atanasio, Luca Pagani, Lauri Saag, Siiri Rootsi, Reedik Magi, Ene Metspalu, Heiki Valk, Martin Malve, Kadri Irdt, Tuuli Reisberg, Anu Solnik, Christiana L. Scheib, Daniel N. Seidman, Amy L. Williams, Kristiina Tambets, Mait Metspalu
Summary: The Finnish population, a genetic isolate, shows unexpected high levels of genetic connectedness with Estonians over the past eight centuries, despite clear differentiation in allele frequencies. This shared genetic heritage may originate from a migration event from North Estonia to Finland between the 8th-10th centuries.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Andaine Seguin-Orlando, Richard Donat, Clio Der Sarkissian, John Southon, Catherine Theves, Claire Manen, Yaramila Tcheremissinoff, Eric Crubezy, Beth Shapiro, Jean-Francois Deleuze, Love Dalen, Jean Guilaine, Ludovic Orlando
Summary: The transition from the Late Neolithic to the Bronze Age in western Europe saw significant population and societal changes, with the genetic diversity of Late Neolithic populations in France revealing heterogeneous hunter-gatherer ancestries and varying genetic contributions from steppe herders. This highlights the complex history of human interactions even at a local scale.
Article
Humanities, Multidisciplinary
Azun Candina Polomer, Ricardo Marzuca Butto
Summary: This article examines the adaptation and integration strategies employed by Arab immigrants in Chile in the first half of the 20th century to combat turcofobia and discrimination, within the prevailing paradigm of Orientalism. Key elements of the process include establishing different institutions, utilizing discursive strategies, engaging in political movements back in their home countries, and fostering a local Arab identity in dialogue with other Arab migrant communities, particularly in Argentina.
MISCELANEA DE ESTUDIOS ARABES Y HEBRAICOS-SECCION ARABE-ISLAM
(2021)
Article
Genetics & Heredity
Hamdi Mbarek, Geethanjali Devadoss Gandhi, Senthil Selvaraj, Wadha Al-Muftah, Radja Badji, Yasser Al-Sarraj, Chadi Saad, Dima Darwish, Muhammad Alvi, Tasnim Fadl, Heba Yasin, Fatima Alkuwari, Rozaimi Razali, Waleed Aamer, Fatemeh Abbaszadeh, Ikhlak Ahmed, Younes Mokrab, Karsten Suhre, Omar Albagha, Khalid Fakhro, Ramin Badii, Said I. Ismail, Asma Althani
Summary: This study describes insights from Phase 1 of the Qatar Genome Program, where 6047 individuals from Qatar were whole genome sequenced. The results show that due to high consanguinity and founder effects in the Middle Eastern population, rare deleterious variants are more common in the Qatari population, while other variants seem to provide protection against diseases and have shaped the genetic architecture of adaptive phenotypes. These findings are valuable for advancing genetic studies in the Arab and neighboring Middle Eastern populations, as well as improving our understanding of global patterns of human variations, human history, and genetic contributions to health and diseases in diverse populations.
Article
Biology
Matthew Metzloff, Emily Yang, Sumit Dhole, Andrew G. Clark, Philipp W. Messer, Jackson Champer
Summary: Our study demonstrates the construction of a tethered drive system in Drosophila, utilizing a locally confined CRISPR Toxin-Antidote Recessive Embryo (TARE) drive to support modification and suppression homing drives. Each drive was able to bias inheritance in its favor, and the TARE drive was shown to spread only when released above a threshold frequency in experimental cage populations. After the TARE drive had established in the population, it facilitated the spread of a subsequently released split homing modification drive (to all individuals in the cage) and of a homing suppression drive (to its equilibrium frequency).
Editorial Material
Genetics & Heredity
Mahbuba Rahman, Herb Schellhorn, Puthen Veetil Jithesh, Md Mizanur Rahman
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Asma A. Elashi, Salman M. Toor, Ilhame Diboun, Yasser Al-Sarraj, Shahrad Taheri, Karsten Suhre, Abdul Badi Abou-Samra, Omar M. E. Albagha
Summary: Maturity-onset diabetes of the young (MODY) is a rare monogenic form of diabetes mellitus. This study estimated the prevalence and genetic spectrum of MODY in the Middle Eastern population of Qatar through whole-genome sequencing, identifying known and potentially novel disease-causing mutations. The study found that MODY accounts for approximately 2.2-3.4% of diabetes patients in Qatar and highlighted the need for further research on the newly identified mutations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Wenqi Cao, Kory C. Douglas, Paul B. Samollow, John L. VandeBerg, Xu Wang, Andrew G. Clark
Summary: Genomic imprinting is a phenomenon that plays important roles in many biological processes, and is only observed in therian mammals. A study investigated the imprinting pattern in marsupials using unbiased RNA-seq studies, discovering and validating 13 imprinted genes, including nine novel imprinted genes. Differential methylation and clustering were observed at marsupial-specific imprinted genes, revealing common mechanisms in the epigenetic regulation of marsupial imprinting.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Sofie Y. N. Delbare, Sara Venkatraman, Kate Scuderi, Martin T. Wells, Mariana F. Wolfner, Sumanta Basu, Andrew G. Clark
Summary: This study used high-resolution time series RNA-sequencing data to explore the genetic architecture of female's response to SP in Drosophila melanogaster. The results showed that SP not only triggers the transcriptional switch in females after mating, but also affects metabolic gene regulatory network and neuronal gene regulatory network, especially the disruption of female's circadian rhythm.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Ikhlak Ahmed, Mubarak Ziab, Sahar Da'as, Waseem Hasan, Sujitha P. Jeya, Elbay Aliyev, Sabah Nisar, Ajaz A. Bhat, Khalid Adnan Fakhro, Ammira S. Alshabeeb Akil
Summary: Diabetic nephropathy (DN) is a common microvascular complication of diabetes that leads to end-stage renal disease. This study aimed to identify key transcription factors (TFs) associated with DN progression by performing a meta-analysis on gene expression profiles from multiple datasets. The analysis revealed distinct clusters of dysregulated susceptibility genes in different renal compartments, with a subset of these genes encoding critical TFs involved in DN development and podocyte function. The role of these TFs was validated in a hyperglycemic zebrafish model, showing that altered expression of these genes leads to morphological abnormalities in various kidney structures. This study provides insights into the molecular drivers, essential genes, and pathways involved in DN initiation and development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Genetics & Heredity
Jullien M. Flynn, Kevin B. Hu, Andrew G. Clark
Summary: This study discovered chromosome fusion and fission events in a strain of D. virilis, leading to genome instability. One substrain with an X-autosome fusion had a 20x higher nondisjunction rate and another substrain with higher satellite DNA had an overall higher DNA breakage rate. These findings suggest a potential role of satellite DNA abundance in genome instability. The establishment of a novel system with four different karyotypes provides a valuable tool for future studies on genome instability, centromere function, and sex chromosome evolution.
Article
Oncology
Angeli Ambayya, Rozaimi Razali, Sarina Sulong, Ezzanie Suffya Zulkefli, Yee Yee Yap, Jameela Sathar, Rosline Hassan
Summary: This study identified genomic biomarkers in AML-NK patients by DNA and RNA sequencing, revealing potential variants affecting gene regulation and functional enrichments. These variants dysregulated transcription and DNA-binding transcription activator activity RNA polymerase II-specific. Characterising genomic variants is crucial for understanding the pathogenesis and heterogeneity of AML-NK.
Article
Psychology, Biological
Iain Mathieson, Felix R. Day, Nicola Barban, Felix C. Tropf, David M. Brazel, Ahmad Vaez, Natalie van Zuydam, Barbara D. Bitarello, Eugene J. Gardner, Evelina T. Akimova, Ajuna Azad, Sven Bergmann, Lawrence F. Bielak, Dorret Boomsma, Kristina Bosak, Marco Brumat, Julie E. Buring, David Cesarini, Daniel Chasman, Jorge E. Chavarro, Massimiliano Cocca, Maria Pina Concas, George Davey Smith, Gail Davies, Ian J. Deary, Tonu Esko, Jessica D. Faul, Oscar Franco, Andrea Ganna, Audrey J. Gaskins, Andrea Gelemanovic, Eco J. C. de Geus, Christian Gieger, Giorgia Girotto, Bamini Gopinath, Hans Joergen Grabe, Erica P. Gunderson, Caroline Hayward, Chunyan He, Diana van Heemst, W. David Hill, Eva R. Hoffmann, Georg Homuth, Jouke Jan Hottenga, Hongyang Huang, Elina Hyppoenen, M. Arfan Ikram, Rick Jansen, Magnus Johannesson, Zoha Kamali, Sharon L. R. Kardia, Maryam Kavousi, Annette Kifley, Tuomo Kiiskinen, Peter Kraft, Brigitte Kuehnel, Claudia Langenberg, Gerald Liew, Penelope A. Lind, Jian'an Luan, Reedik Magi, Patrik K. E. Magnusson, Anubha Mahajan, Nicholas G. Martin, Hamdi Mbarek, Mark McCarthy, George McMahon, Sarah E. Medland, Thomas Meitinger, Andres Metspalu, Evelin Mihailov, Lili Milani, Stacey A. Missmer, Paul Mitchell, Stine Mollegaard, Dennis O. Mook-Kanamori, Anna Morgan, Peter van der Most, Renee de Mutsert, Matthias Nauck, Ilja M. Nolte, Raymond Noordam, Brenda W. J. H. Penninx, Annette Peters, Patricia A. Peyser, Ozren Polasek, Chris Power, Ajka Pribisalic, Paul Redmond, Janet W. Rich-Edwards, Paul M. Ridker, Cornelius A. Rietveld, Susan M. Ring, Lynda M. Rose, Rico Rueedi, Vallari Shukla, Jennifer A. Smith, Stasa Stankovic, Kari Stefansson, Doris Stoeckl, Konstantin Strauch, Morris A. Swertz, Alexander Teumer, Gudmar Thorleifsson, Unnur Thorsteinsdottir, A. Roy Thurik, Nicholas J. Timpson, Constance Turman, Andre G. Uitterlinden, Melanie Waldenberger, Nicholas J. Wareham, David R. Weir, Gonneke Willemsen, Jing Hau Zhao, Wei Zhao, Yajie Zhao, Harold Snieder, Marcel den Hoed, Ken K. Ong, Melinda C. Mills, John R. B. Perry
Summary: Identifying genetic determinants of reproductive success can reveal the mechanisms underlying fertility and identify genes that are currently under natural selection. A genome-wide association study on individuals of European ancestry identified 43 genomic loci associated with the number of children ever born or childlessness. These loci are involved in various aspects of reproductive biology, such as puberty timing, age at first birth, sex hormone regulation, endometriosis, and age at menopause. Additionally, missense variants in ARHGAP27 were found to be associated with higher number of children ever born but shorter reproductive lifespan, suggesting a trade-off at this locus. Other genes, including PIK3IP1, ZFP82, and LRP4, were also implicated by coding variants, and a new role for the melanocortin 1 receptor (MC1R) in reproductive biology was suggested. Furthermore, integration with data from historical selection scans revealed an allele in the FADS1/2 gene locus that has been undergoing selection for thousands of years. These findings highlight the diverse biological mechanisms contributing to reproductive success.
NATURE HUMAN BEHAVIOUR
(2023)
Article
Biochemistry & Molecular Biology
Gehan H. Heeba, Mohamed A. Morsy, Magda E. Mahmoud, Rania Abdel-latif
Summary: This study found that L-arginine could protect against gastric ulceration induced by indomethacin. It enhanced the levels of nitric oxide and prostaglandin E2 in gastric mucosa and suppressed gastric inflammation and oxidative stress.
JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY
(2023)
Article
Nutrition & Dietetics
Nagham Nafiz Hendi, Marlene Chakhtoura, Yasser Al-Sarraj, Dania Saleh Basha, Omar Albagha, Ghada El-Hajj Fuleihan, Georges Nemer
Summary: The Middle East region has a high prevalence of vitamin D deficiency, particularly among elderly individuals. Genetic studies on vitamin D have focused mostly on European populations, therefore there is a lack of research on the genetic factors affecting elderly people in the Middle East. In this study, we identified novel genomic loci associated with vitamin D levels in elderly Lebanese individuals and confirmed the replication of numerous variants from a European study. Our findings provide new insights into the genetic mechanisms of vitamin D deficiency in elderly Middle Eastern populations and can aid in the development of personalized approaches for its management.
Article
Genetics & Heredity
Mona Abdi, Elbay Aliyev, Brett Trost, Muhammad Kohailan, Waleed Aamer, Najeeb Syed, Rulan Shaath, Geethanjali Devadoss Gandhi, Worrawat Engchuan, Jennifer Howe, Bhooma Thiruvahindrapuram, Melissa Geng, Joe Whitney, Amira Syed, Jyothi Lakshmi, Sura Hussein, Najwa Albashir, Amal Hussein, Ilaria Poggiolini, Saba F. Elhag, Sasirekha Palaniswamy, Marios Kambouris, Maria de Fatima Janjua, Mohamed O. El Tahir, Ahsan Nazeer, Durre Shahwar, Muhammad Waqar Azeem, Younes Mokrab, Nazim Abdel Aati, Ammira Akil, Stephen W. Scherer, Madeeha Kamal, Khalid A. Fakhro
Summary: This study identified potentially pathogenic variants in ASD families in Qatar, with a significant proportion being single-gene variants. It also highlighted the impact of recessive variation on the ASD architecture in consanguineous settings, providing a unique genomic resource for future ASD research in the global community.
Article
Biochemistry & Molecular Biology
Salman M. Toor, Eman K. Aldous, Aijaz Parray, Naveed Akhtar, Yasser Al-Sarraj, Essam M. Abdelalim, Abdelilah Arredouani, Omar El-Agnaf, Paul J. Thornalley, Sajitha V. Pananchikkal, Ghulam Jeelani Pir, Raheem Ayadathil, Ashfaq Shuaib, Nehad M. Alajez, Omar M. E. Albagha
Summary: Transient ischemic attack (TIA) is a temporary neurologic deficit caused by ischemic insult to the brain, spinal cord, or retina. TIA is associated with a high risk of impending acute ischemic stroke (AIS), a condition characterized by focal infarction in the brain, spinal cord, or retina. This study investigated the differences in circulating microRNA profiles between AIS and TIA patients and identified a panel of differentially regulated microRNAs. Furthermore, a multivariate classifier was developed that could potentially be used as a biomarker to distinguish AIS and TIA patients. Understanding the molecular pathways in AIS compared to TIA may have important implications for therapeutic targeting in clinical translation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Obstetrics & Gynecology
Hamdi Mbarek, Scott D. Gordon, David L. Duffy, Nikki Hubers, Sally Mortlock, Jeffrey J. Beck, Jouke-Jan Hottenga, Rene Pool, Conor Dolan, Ky'Era Actkins, Zachary F. Gerring, Jenny Van Dongen, Erik A. Ehli, William G. Iacono, Matt Mcgue, Daniel Chasman, C. Scott Gallagher, Samantha L. P. Schilit, Cynthia C. Morton, Guillaume Pare, Gonneke Willemsen, David C. Whiteman, Catherine M. Olsen, Catherine Derom, Robert Vlietinck, Daniel Gudbjartsson, Lisa Cannon-Albright, Eva Krapohl, Robert Plomin, Patrik K. E. Magnusson, Nancy L. Pedersen, Pirro Hysi, Massimo Mangino, Timothy D. Spector, Teemu Palviainen, Yuri Milaneschi, Brenda W. Penninnx, Adrian Campos, Ken K. Ong, John R. B. Perry, Cornelis B. Lambalk, Jaakko Kaprio, Isleifur Olafsson, Karine Duroure, Celine Revenu, Miguel E. Renteria, Loic Yengo, Lea Davis, Eske M. Derks, Sarah E. Medland, Hreinn Stefansson, Kari Stefansson, Filippo Del Bene, Bruno Reversade, Grant W. Montgomery, Dorret Boomsma, Nicholas G. Martin
Summary: This study identified four new loci associated with female propensity for giving birth to spontaneous dizygotic twins. The novel loci, GNRH1 and FSHR, have established roles in female reproduction, while ZFPM1 and IPO8 were not previously linked to female fertility. The study also found significant genetic correlations with multiple aspects of female reproduction and body size, suggesting important roles in human evolution.
HUMAN REPRODUCTION
(2023)