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Venkatesh SS, Wittemans LBL, Palmer DS, Baya NA, Ferreira T, Hill B, Lassen FH, Parker MJ, Reibe S, Elhakeem A, Banasik K, Bruun MT, Erikstrup C, Jensen BA, Juul A, Mikkelsen C, Nielsen HS, Ostrowski SR, Pedersen OB, Rohde PD, Sorensen E, Ullum H, Westergaard D, Haraldsson A, Holm H, Jonsdottir I, Olafsson I, Steingrimsdottir T, Steinthorsdottir V, Thorleifsson G, Figueredo J, Karjalainen MK, Pasanen A, Jacobs BM, Hubers N, Lippincott M, Fraser A, Lawlor DA, Timpson NJ, Nyegaard M, Stefansson K, Magi R, Laivuori H, van Heel DA, Boomsma DI, Balasubramanian R, Seminara SB, Chan YM, Laisk T, Lindgren CM. Genome-wide analyses identify 21 infertility loci and over 400 reproductive hormone loci across the allele frequency spectrum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.19.24304530. [PMID: 38562841 PMCID: PMC10984039 DOI: 10.1101/2024.03.19.24304530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genome-wide association studies (GWASs) may help inform treatments for infertility, whose causes remain unknown in many cases. Here we present GWAS meta-analyses across six cohorts for male and female infertility in up to 41,200 cases and 687,005 controls. We identified 21 genetic risk loci for infertility (P≤5E-08), of which 12 have not been reported for any reproductive condition. We found positive genetic correlations between endometriosis and all-cause female infertility (rg=0.585, P=8.98E-14), and between polycystic ovary syndrome and anovulatory infertility (rg=0.403, P=2.16E-03). The evolutionary persistence of female infertility-risk alleles in EBAG9 may be explained by recent directional selection. We additionally identified up to 269 genetic loci associated with follicle-stimulating hormone (FSH), luteinising hormone, oestradiol, and testosterone through sex-specific GWAS meta-analyses (N=6,095-246,862). While hormone-associated variants near FSHB and ARL14EP colocalised with signals for anovulatory infertility, we found no rg between female infertility and reproductive hormones (P>0.05). Exome sequencing analyses in the UK Biobank (N=197,340) revealed that women carrying testosterone-lowering rare variants in GPC2 were at higher risk of infertility (OR=2.63, P=1.25E-03). Taken together, our results suggest that while individual genes associated with hormone regulation may be relevant for fertility, there is limited genetic evidence for correlation between reproductive hormones and infertility at the population level. We provide the first comprehensive view of the genetic architecture of infertility across multiple diagnostic criteria in men and women, and characterise its relationship to other health conditions.
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Affiliation(s)
- Samvida S Venkatesh
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Laura B L Wittemans
- Novo Nordisk Research Centre Oxford, Oxford, United Kingdom
- Nuffield Department of Women's and Reproductive Health, Medical Sciences Division, University of Oxford, United Kingdom
| | - Duncan S Palmer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Nikolas A Baya
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Teresa Ferreira
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Barney Hill
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Frederik Heymann Lassen
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Melody J Parker
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Saskia Reibe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Nuffield Department of Population Health, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Ahmed Elhakeem
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark
| | - Mie T Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Health, Aarhus University, Aarhus, Denmark
| | - Bitten A Jensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Anders Juul
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen; Copenhagen, Denmark
- Department of Growth and Reproduction, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Christina Mikkelsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, Copenhagen University, Copenhagen, Denmark
| | - Henriette S Nielsen
- Department of Obstetrics and Gynecology, The Fertility Clinic, Hvidovre University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole B Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Kge, Denmark
| | - Palle D Rohde
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Erik Sorensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark
| | - Asgeir Haraldsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Children's Hospital Iceland, Landspitali University Hospital, Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Ingileif Jonsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik, Iceland
| | - Thora Steingrimsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | - Jessica Figueredo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Minna K Karjalainen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Finland
- Northern Finland Birth Cohorts, Arctic Biobank, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Anu Pasanen
- Research Unit of Clinical Medicine, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Benjamin M Jacobs
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, EC1M 6BQ, United Kingdom
| | - Nikki Hubers
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Institute, Amsterdam, The Netherlands
| | - Margaret Lippincott
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Abigail Fraser
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Mette Nyegaard
- Genomic Medicine, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Kari Stefansson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
| | - Reedik Magi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital, Finland
- Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - David A van Heel
- Blizard Institute, Queen Mary University London, London, E1 2AT, United Kingdom
| | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Institute, Amsterdam, The Netherlands
| | - Ravikumar Balasubramanian
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephanie B Seminara
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yee-Ming Chan
- Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, United States of America
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cecilia M Lindgren
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
- Nuffield Department of Women's and Reproductive Health, Medical Sciences Division, University of Oxford, United Kingdom
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
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Papiris SA, Veith M, Papaioannou AI, Apollonatou V, Ferrarotti I, Ottaviani S, Tzouvelekis A, Tzilas V, Rovina N, Stratakos G, Gerogianni I, Daniil Z, Kolilekas L, Dimakou K, Pitsidianakis G, Tzanakis N, Tryfon S, Fragopoulos F, Antonogiannaki EM, Lazaratou A, Fouka E, Papakosta D, Emmanouil P, Anagnostopoulos N, Karampitsakos T, Vlami K, Kallieri M, Lyberopoulos P, Loukides S, Bouros D, Bush A, Balduyck M, Lombard C, Cottin V, Mornex JF, Vogelmeier CF, Greulich T, Manali ED. Alpha1-antitrypsin deficiency in Greece: Focus on rare variants. Pulmonology 2024; 30:43-52. [PMID: 36797151 DOI: 10.1016/j.pulmoe.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 02/16/2023] Open
Abstract
PURPOSE A1Antitrypsin deficiency (AATD) pathogenic mutations are expanding beyond the PI*Z and PI*S to a multitude of rare variants. AIM to investigate genotype and clinical profile of Greeks with AATD. METHODS Symptomatic adult-patients with early-emphysema defined by fixed airway obstruction and computerized-tomography scan and lower than normal serum AAT levels were enrolled from reference centers all over Greece. Samples were analyzed in the AAT Laboratory, University of Marburg-Germany. RESULTS Included are 45 adults, 38 homozygous or compound heterozygous for pathogenic variants and 7 heterozygous. Homozygous were 57.9% male, 65.8% ever-smokers, median (IQR) age 49.0(42.5-58.5) years, AAT-levels 0.20(0.08-0.26) g/L, FEV1(%predicted) 41.5(28.8-64.5). PI*Z, PI*Q0, and rare deficient allele's frequency was 51.3%, 32.9%,15.8%, respectively. PI*ZZ genotype was 36.8%, PI*Q0Q0 21.1%, PI*MdeficientMdeficient 7.9%, PI*ZQ0 18.4%, PI*Q0Mdeficient 5.3% and PI*Zrare-deficient 10.5%. Genotyping by Luminex detected: p.(Pro393Leu) associated with MHeerlen (M1Ala/M1Val); p.(Leu65Pro) with MProcida; p.(Lys241Ter) with Q0Bellingham; p.(Leu377Phefs*24) with Q0Mattawa (M1Val) and Q0Ourem (M3); p.(Phe76del) with MMalton (M2), MPalermo (M1Val), MNichinan (V) and Q0LaPalma (S); p.(Asp280Val) with PLowell (M1Val); PDuarte (M4), YBarcelona (p.Pro39His). Gene-sequencing (46.7%) detected Q0GraniteFalls, Q0Saint-Etienne, Q0Amersfoort(M1Ala), MWürzburg, NHartfordcity and one novel-variant (c.1A>G) named Q0Attikon.Heterozygous included PI*MQ0Amersfoort(M1Ala), PI*MMProcida, PI*Mp.(Asp280Val), PI*MOFeyzin. AAT-levels were significantly different between genotypes (p = 0.002). CONCLUSION Genotyping AATD in Greece, a multiplicity of rare variants and a diversity of rare combinations, including unique ones were observed in two thirds of patients, expanding knowledge regarding European geographical trend in rare variants. Gene sequencing was necessary for genetic diagnosis. In the future the detection of rare genotypes may add to personalize preventive and therapeutic measures.
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Affiliation(s)
- S A Papiris
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece.
| | - M Veith
- Department of Medicine, Pulmonary and Critical Care Medicine, Member of the German Center for Lung Research (DZL), UKGM, Marburg, Germany
| | - A I Papaioannou
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - V Apollonatou
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - I Ferrarotti
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, Pneumonology Unit, Fondazione IRCCS Policlinico San Matteo, Università di Pavia, Pavia, Italy
| | - S Ottaviani
- Center for Diagnosis of Inherited Alpha1-antitrypsin Deficiency, Department of Internal Medicine and Therapeutics, Pneumonology Unit, Fondazione IRCCS Policlinico San Matteo, Università di Pavia, Pavia, Italy
| | - A Tzouvelekis
- Department of Respiratory Medicine, General Hospital of Patras, University of Patras, Greece
| | - V Tzilas
- 5th Pulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece
| | - N Rovina
- 1st Department of Pulmonary Medicine and Intensive Care Unit, Medical School, National and Kapodistrian University of Athens, Athens 115 27, Greece
| | - G Stratakos
- 1st Respiratory Medicine Department of the National, Kapodistrian University of Athens, Athens, Greece
| | - I Gerogianni
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa Greece
| | - Z Daniil
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa Greece
| | - L Kolilekas
- 7thPulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece
| | - K Dimakou
- 5th Pulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece
| | - G Pitsidianakis
- Department of Thoracic Medicine, University Hospital, University of Crete, Heraklion, Crete 71110, Greece
| | - N Tzanakis
- Department of Thoracic Medicine, University Hospital, University of Crete, Heraklion, Crete 71110, Greece
| | - S Tryfon
- General Hospital "G. Papanikolaou", Thessaloniki, Greece
| | - F Fragopoulos
- Pulmonary Department, General Hospital of Nicosia, Cyprus
| | - E M Antonogiannaki
- 4th Pulmonary Department, Athens Chest Hospital "Sotiria", Athens Greece
| | - A Lazaratou
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - E Fouka
- A Department of Pulmonary Medicine, Aristotle University of Thessaloniki, "G. Papanikolaou" Hospital, Exochi, Thessaloniki, Greece
| | - D Papakosta
- A Department of Pulmonary Medicine, Aristotle University of Thessaloniki, "G. Papanikolaou" Hospital, Exochi, Thessaloniki, Greece
| | | | - N Anagnostopoulos
- 1st Respiratory Medicine Department of the National, Kapodistrian University of Athens, Athens, Greece
| | - T Karampitsakos
- Department of Respiratory Medicine, General Hospital of Patras, University of Patras, Greece
| | - K Vlami
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - M Kallieri
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - P Lyberopoulos
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - S Loukides
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
| | - D Bouros
- Iatriko Medical Center, Athens, Greece; School of Medicine, National and Kapodistrian University of Athens, Athens Greece
| | - A Bush
- Paediatrics and Paediatric Respirology, Imperial College, Imperial Centre for Paediatrics and Child Health, Royal Brompton Harefield NHS Foundation Trust, London, United Kingdom
| | - M Balduyck
- laboratoire de Biochimie et Biologie Moléculaire (HMNO), Centre de Biologie Pathologie, Faculté de pharmacie et EA 7364 RADEME, Laboratoire de Biochimie et Biologie Moléculaire, CHU de Lille, Université de Lille, Lille, France
| | - C Lombard
- Laboratoire d'Immunologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon and Université Claude Bernard-Lyon 1, Lyon, France
| | - V Cottin
- Service de pneumologie, Centre National Coordinateur de Référence des Maladies Pulmonaires Rares, Hôpital Louis Pradel, Hospices Civils de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, UMR754 INRA, IVPC, Lyon, France
| | - J F Mornex
- Service de pneumologie, Centre National Coordinateur de Référence des Maladies Pulmonaires Rares, Hôpital Louis Pradel, Hospices Civils de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, UMR754 INRA, IVPC, Lyon, France
| | - C F Vogelmeier
- Department of Medicine, Pulmonary and Critical Care Medicine, Member of the German Center for Lung Research (DZL), UKGM, Marburg, Germany
| | - T Greulich
- Department of Medicine, Pulmonary and Critical Care Medicine, Member of the German Center for Lung Research (DZL), UKGM, Marburg, Germany
| | - E D Manali
- 2nd Pulmonary Medicine Department, Medical School, General University Hospital "Attikon", National and Kapodistrian University of Athens, Greece 1 Rimini Street, Haidari 12462, Greece
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Wilke F, Herrick N, Matthews H, Hoskens H, Singh S, Shaffer JR, Weinberg SM, Shriver MD, Claes P, Walsh S. Exploring regional aspects of 3D facial variation within European individuals. Sci Rep 2023; 13:3708. [PMID: 36879022 PMCID: PMC9988837 DOI: 10.1038/s41598-023-30855-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Facial ancestry can be described as variation that exists in facial features that are shared amongst members of a population due to environmental and genetic effects. Even within Europe, faces vary among subregions and may lead to confounding in genetic association studies if unaccounted for. Genetic studies use genetic principal components (PCs) to describe facial ancestry to circumvent this issue. Yet the phenotypic effect of these genetic PCs on the face has yet to be described, and phenotype-based alternatives compared. In anthropological studies, consensus faces are utilized as they depict a phenotypic, not genetic, ancestry effect. In this study, we explored the effects of regional differences on facial ancestry in 744 Europeans using genetic and anthropological approaches. Both showed similar ancestry effects between subgroups, localized mainly to the forehead, nose, and chin. Consensus faces explained the variation seen in only the first three genetic PCs, differing more in magnitude than shape change. Here we show only minor differences between the two methods and discuss a combined approach as a possible alternative for facial scan correction that is less cohort dependent, more replicable, non-linear, and can be made open access for use across research groups, enhancing future studies in this field.
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Affiliation(s)
- Franziska Wilke
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA
| | - Noah Herrick
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA
| | - Harold Matthews
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
| | - Sylvia Singh
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
| | - Peter Claes
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W Michigan St, Indianapolis, IN, 46202, USA.
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Jankowski M, Daca-Roszak P, Obracht-Prondzyński C, Płoski R, Lipska-Ziętkiewicz BS, Ziętkiewicz E. Genetic diversity in Kashubs: the regional increase in the frequency of several disease-causing variants. J Appl Genet 2022; 63:691-701. [PMID: 35971028 PMCID: PMC9637066 DOI: 10.1007/s13353-022-00713-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 12/02/2022]
Abstract
Differential distribution of genetic variants’ frequency among human populations is caused by the genetic drift in isolated populations, historical migrations, and demography. Some of these variants are identical by descent and represent founder mutations, which — if pathogenic in nature — lead to the increased frequency of otherwise rare diseases. The detection of the increased regional prevalence of pathogenic variants may shed light on the historical processes that affected studied populations and can help to develop effective screening and diagnostic strategies as a part of personalized medicine. Here, we discuss the specific genetic diversity in Kashubs, the minority group living in northern Poland, reflected in the biased distribution of some of the repetitively found disease-causing variants. These include the following: (1) c.662A > G (p.Asp221Gly) in LDLR, causing heterozygous familial hypercholesterolemia; (2) c.3700_3704del in BRCA1, associated with hereditary breast and ovarian cancer syndrome; (3) c.1528G > C (p.Glu510Gln) in HADHA, seen in long-chain 3-hydroxy acyl-CoA dehydrogenase (LCHAD) deficiency, and (4) c.1032delT in NPHS2, associated with steroid-resistant nephrotic syndrome.
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Affiliation(s)
- Maciej Jankowski
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | | | | | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Beata S Lipska-Ziętkiewicz
- Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland. .,Centre for Rare Diseases, Medical University of Gdansk, Gdansk, Poland.
| | - Ewa Ziętkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.
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5
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Chen A, Luo L, Tao R, Zhang S, Li C. Forensic parameters of 41 Y-STR loci in Shandong Han individuals and comparison with 42 other populations. Forensic Sci Res 2021; 7:823-825. [PMID: 36817248 PMCID: PMC9930784 DOI: 10.1080/20961790.2021.1963397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Anqi Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Li Luo
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China,CONTACT Suhua Zhang ;
| | - Chengtao Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China,Chengtao Li
Supplemental data for this article can be accessed online at https://doi.org/10.1080/20961790.2021.1963397.
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Masuda R, Lodge S, Nitschke P, Spraul M, Schaefer H, Bong SH, Kimhofer T, Hall D, Loo RL, Bizkarguenaga M, Bruzzone C, Gil-Redondo R, Embade N, Mato JM, Holmes E, Wist J, Millet O, Nicholson JK. Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts. J Proteome Res 2021; 20:4139-4152. [PMID: 34251833 DOI: 10.1021/acs.jproteome.1c00458] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quantitative plasma lipoprotein and metabolite profiles were measured on an autonomous community of the Basque Country (Spain) cohort consisting of hospitalized COVID-19 patients (n = 72) and a matched control group (n = 75) and a Western Australian (WA) cohort consisting of (n = 17) SARS-CoV-2 positives and (n = 20) healthy controls using 600 MHz 1H nuclear magnetic resonance (NMR) spectroscopy. Spanish samples were measured in two laboratories using one-dimensional (1D) solvent-suppressed and T2-filtered methods with in vitro diagnostic quantification of lipoproteins and metabolites. SARS-CoV-2 positive patients and healthy controls from both populations were modeled and cross-projected to estimate the biological similarities and validate biomarkers. Using the top 15 most discriminatory variables enabled construction of a cross-predictive model with 100% sensitivity and specificity (within populations) and 100% sensitivity and 82% specificity (between populations). Minor differences were observed between the control metabolic variables in the two cohorts, but the lipoproteins were virtually indistinguishable. We observed highly significant infection-related reductions in high-density lipoprotein (HDL) subfraction 4 phospholipids, apolipoproteins A1 and A2,that have previously been associated with negative regulation of blood coagulation and fibrinolysis. The Spanish and Australian diagnostic SARS-CoV-2 biomarkers were mathematically and biologically equivalent, demonstrating that NMR-based technologies are suitable for the study of the comparative pathology of COVID-19 via plasma phenotyping.
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Affiliation(s)
- Reika Masuda
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Samantha Lodge
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Philipp Nitschke
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Manfred Spraul
- Bruker Biospin GmbH, Silberstreifen, Ettlingen 76275, Germany
| | | | - Sze-How Bong
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Torben Kimhofer
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Drew Hall
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Ruey Leng Loo
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Maider Bizkarguenaga
- CIC bioGUNE, Asociación Centro de Investigación Cooperativa en Biociencias, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Chiara Bruzzone
- CIC bioGUNE, Asociación Centro de Investigación Cooperativa en Biociencias, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Rubén Gil-Redondo
- CIC bioGUNE, Asociación Centro de Investigación Cooperativa en Biociencias, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Nieves Embade
- CIC bioGUNE, Asociación Centro de Investigación Cooperativa en Biociencias, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - José M Mato
- CIC bioGUNE, Asociación Centro de Investigación Cooperativa en Biociencias, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Elaine Holmes
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Section for Nutrition Research, Department of Metabolism, Nutrition and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, U.K
| | - Julien Wist
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Chemistry Department, Universidad del Valle, 76001 Cali, Colombia
| | - Oscar Millet
- CIC bioGUNE, Asociación Centro de Investigación Cooperativa en Biociencias, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Jeremy K Nicholson
- Australian National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia.,Institute of Global Health Innovation, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, U.K
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Seixas S, Marques PI. Known Mutations at the Cause of Alpha-1 Antitrypsin Deficiency an Updated Overview of SERPINA1 Variation Spectrum. APPLICATION OF CLINICAL GENETICS 2021; 14:173-194. [PMID: 33790624 PMCID: PMC7997584 DOI: 10.2147/tacg.s257511] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
Alpha-1-Antitrypsin deficiency (AATD), caused by SERPINA1 mutations, is one of the most prevalent Mendelian disorders among individuals of European descend. However, this condition, which is characterized by reduced serum levels of alpha-1-antitrypsin (AAT) and associated with increased risks of pulmonary emphysema and liver disease in both children and adults, remains frequently underdiagnosed. AATD clinical manifestations are often correlated with two pathogenic variants, the Z allele (p.Glu342Lys) and the S allele (p.Glu264Val), which can be combined in severe ZZ or moderate SZ risk genotypes. Yet, screenings of AATD cases and large sequencing efforts carried out in both control and disease populations are disclosing outstanding numbers of rare SERPINA1 variants (>500), including many pathogenic and other likely deleterious mutations. Generally speaking, pathogenic variants can be subdivided into either loss- or gain-of-function according to their pathophysiological effects. In AATD, the loss-of-function is correlated with an uncontrolled activity of elastase by its natural inhibitor, the AAT. This phenomenon can result from the absence of circulating AAT (null alleles), poor AAT secretion from hepatocytes (deficiency alleles) or even from a modified inhibitory activity (dysfunctional alleles). On the other hand, the gain-of-function is connected with the formation of AAT polymers and their switching on of cellular stress and inflammatory responses (deficiency alleles). Less frequently, the gain-of-function is related to a modified protease affinity (dysfunctional alleles). Here, we revisit SERPINA1 mutation spectrum, its origins and population history with a greater emphasis on variants fitting the aforementioned processes of AATD pathogenesis. Those were selected based on their clinical significance and wider geographic distribution. Moreover, we also provide some directions for future studies of AATD clinically heterogeneity and comprehensive diagnosis.
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Affiliation(s)
- Susana Seixas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Patricia Isabel Marques
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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8
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Harris EE. Demic and cultural diffusion in prehistoric Europe in the age of ancient genomes. Evol Anthropol 2017; 26:228-241. [PMID: 29027332 DOI: 10.1002/evan.21545] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2017] [Indexed: 11/10/2022]
Abstract
Ancient genomes can help us detect prehistoric migrations, population contractions, and admixture among populations. Knowing the dynamics of demography is invaluable for understanding culture change in prehistory, particularly the roles played by demic and cultural diffusion in transformations of material cultures. Prehistoric Europe is a region where ancient genome analyses can help illuminate the interplay between demography and culture change. In Europe, there is more archeological evidence, in terms of detailed studies, radiometric dates, and explanatory hypotheses that can be evaluated, than in any other region of the world. Here I show some important ways that ancient genomes have given us insights into population movements in European prehistory. I also propose that studies might be increasingly focused on specific questions of culture change, for example in evaluating the makers of "transitional" industries as well as the origins of the Gravettian and spread of the Magdalenian. I also discuss genomic evidence supporting the large role that demic expansion has played in the Neolithization of Europe and the formation of the European population during the Bronze Age.
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Affiliation(s)
- Eugene E Harris
- Department of Biological Sciences and Geology, Queensborough Community College, City University of New York, Medical Arts Building, M-213, 222-05, 56th Avenue Bayside, NY, 1136411364.,Affiliated Researcher, Center for the Study of Human Origins, New York University
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Heath KM, Axton JH, McCullough JM, Harris N. The evolutionary adaptation of the C282Y mutation to culture and climate during the European Neolithic. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:86-101. [PMID: 26799452 PMCID: PMC5066702 DOI: 10.1002/ajpa.22937] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 12/20/2015] [Accepted: 12/20/2015] [Indexed: 01/10/2023]
Abstract
OBJECTIVES The C282Y allele is the major cause of hemochromatosis as a result of excessive iron absorption. The mutation arose in continental Europe no earlier than 6,000 years ago, coinciding with the arrival of the Neolithic agricultural revolution. Here we hypothesize that this new Neolithic diet, which originated in the sunny warm and dry climates of the Middle East, was carried by migrating farmers into the chilly and damp environments of Europe where iron is a critical micronutrient for effective thermoregulation. We argue that the C282Y allele was an adaptation to this novel environment. MATERIALS AND METHODS To address our hypothesis, we compiled C282Y allele frequencies, known Neolithic sites in Europe and climatic data on temperature and rainfall for statistical analysis. RESULTS Our findings indicate that the geographic cline for C282Y frequency in Europe increases as average temperatures decrease below 16°C, a critical threshold for thermoregulation, with rainy days intensifying the trend. DISCUSSION The results indicate that the deleterious C282Y allele, responsible for most cases of hemochromatosis, may have evolved as a selective advantage to culture and climate during the European Neolithic.
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Affiliation(s)
- Kathleen M. Heath
- Department of Earth and Environmental SystemsIndiana State UniversityTerre HauteIN47809
| | - Jacob H. Axton
- Department of BiologyIndiana State UniversityTerre HauteIN47809
| | | | - Nathan Harris
- Department of AnthropologyUniversity of UtahSalt Lake CityUT84112
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Chakravarti A. Perspectives on Human Variation through the Lens of Diversity and Race. Cold Spring Harb Perspect Biol 2015; 7:a023358. [PMID: 26330522 PMCID: PMC4563709 DOI: 10.1101/cshperspect.a023358] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human populations, however defined, differ in the distribution and frequency of traits they display and diseases to which individuals are susceptible. These need to be understood with respect to three recent advances. First, these differences are multicausal and a result of not only genetic but also epigenetic and environmental factors. Second, the actions of genes, although crucial, turn out to be quite dynamic and modifiable, which contrasts with the classical view that they are inflexible machines. Third, the diverse human populations across the globe have spent too little time apart from our common origin 50,000 years ago to have developed many individually adapted traits. Human trait and disease differences by continental ancestry are thus as much the result of nongenetic as genetic forces.
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Affiliation(s)
- Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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