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Article ; Online: The human genetic epidemiology of COVID-19.

Niemi, Mari E K / Daly, Mark J / Ganna, Andrea

2022 Volume 23, Issue 9, Page(s) 533–546

Abstract: Human genetics can inform the biology and epidemiology of coronavirus disease 2019 (COVID-19) by pinpointing causal mechanisms that explain why some individuals become more severely affected by the disease upon infection by the severe acute respiratory ... ...

Abstract	Human genetics can inform the biology and epidemiology of coronavirus disease 2019 (COVID-19) by pinpointing causal mechanisms that explain why some individuals become more severely affected by the disease upon infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Large-scale genetic association studies, encompassing both rare and common genetic variants, have used different study designs and multiple disease phenotype definitions to identify several genomic regions associated with COVID-19. Along with a multitude of follow-up studies, these findings have increased our understanding of disease aetiology and provided routes for management of COVID-19. Important emergent opportunities include the clinical translatability of genetic risk prediction, the repurposing of existing drugs, exploration of variable host effects of different viral strains, study of inter-individual variability in vaccination response and understanding the long-term consequences of SARS-CoV-2 infection. Beyond the current pandemic, these transferrable opportunities are likely to affect the study of many infectious diseases.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/genetics ; Humans ; Molecular Epidemiology ; Pandemics ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-05-02
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2035157-4
ISSN	1471-0064 ; 1471-0056
ISSN (online)	1471-0064
ISSN	1471-0056
DOI	10.1038/s41576-022-00478-5
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Article ; Online: Reduced reproductive success is associated with selective constraint on human genes.

Gardner, Eugene J / Neville, Matthew D C / Samocha, Kaitlin E / Barclay, Kieron / Kolk, Martin / Niemi, Mari E K / Kirov, George / Martin, Hilary C / Hurles, Matthew E

Nature

2022 Volume 603, Issue 7903, Page(s) 858–863

Abstract: Genome-wide sequencing of human populations has revealed substantial variation among genes in the intensity of purifying selection acting on damaging genetic ... ...

Abstract	Genome-wide sequencing of human populations has revealed substantial variation among genes in the intensity of purifying selection acting on damaging genetic variants
MeSH term(s)	Chromosome Mapping ; Female ; Heterozygote ; Humans ; Male ; Phenotype ; Reproduction/genetics ; Selection, Genetic
Language	English
Publishing date	2022-03-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-022-04549-9
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Article ; Online: Solanidine is a sensitive and specific dietary biomarker for CYP2D6 activity.

Kiiski, Johanna I / Neuvonen, Mikko / Kurkela, Mika / Hirvensalo, Päivi / Hämäläinen, Kreetta / Tarkiainen, E Katriina / Sistonen, Johanna / Korhonen, Mari / Khan, Sofia / Orpana, Arto / Filppula, Anne M / Lehtonen, Marko / Niemi, Mikko

Human genomics

2024 Volume 18, Issue 1, Page(s) 11

Abstract: Background: Individual assessment of CYP enzyme activities can be challenging. Recently, the potato alkaloid solanidine was suggested as a biomarker for CYP2D6 activity. Here, we aimed to characterize the sensitivity and specificity of solanidine as a ... ...

Abstract	Background: Individual assessment of CYP enzyme activities can be challenging. Recently, the potato alkaloid solanidine was suggested as a biomarker for CYP2D6 activity. Here, we aimed to characterize the sensitivity and specificity of solanidine as a CYP2D6 biomarker among Finnish volunteers with known CYP2D6 genotypes. Results: Using non-targeted metabolomics analysis, we identified 9152 metabolite features in the fasting plasma samples of 356 healthy volunteers. Machine learning models suggested strong association between CYP2D6 genotype-based phenotype classes with a metabolite feature identified as solanidine. Plasma solanidine concentration was 1887% higher in genetically poor CYP2D6 metabolizers (gPM) (n = 9; 95% confidence interval 755%, 4515%; P = 1.88 × 10 Conclusions: These results are in line with earlier studies and further indicate that solanidine and its metabolites are sensitive and specific biomarkers for measuring CYP2D6 activity. Since potato consumption is common worldwide, this biomarker could be useful for evaluating CYP2D6-mediated drug-drug interactions and to improve prediction of CYP2D6 activity in addition to genotyping.
MeSH term(s)	Humans ; Cytochrome P-450 CYP2D6/genetics ; Genome-Wide Association Study ; Paroxetine/pharmacology ; Biomarkers ; Genotype ; Diosgenin
Chemical Substances	Cytochrome P-450 CYP2D6 (EC 1.14.14.1) ; solanidine (W7801OHM8B) ; Paroxetine (41VRH5220H) ; Biomarkers ; Diosgenin (K49P2K8WLX)
Language	English
Publishing date	2024-02-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2147618-4
ISSN	1479-7364 ; 1479-7364
ISSN (online)	1479-7364
ISSN	1479-7364
DOI	10.1186/s40246-024-00579-8
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Article ; Online: The contribution of X-linked coding variation to severe developmental disorders.

Martin, Hilary C / Gardner, Eugene J / Samocha, Kaitlin E / Kaplanis, Joanna / Akawi, Nadia / Sifrim, Alejandro / Eberhardt, Ruth Y / Tavares, Ana Lisa Taylor / Neville, Matthew D C / Niemi, Mari E K / Gallone, Giuseppe / McRae, Jeremy / Wright, Caroline F / FitzPatrick, David R / Firth, Helen V / Hurles, Matthew E

Nature communications

2021 Volume 12, Issue 1, Page(s) 627

Abstract: Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11, ... ...

Abstract	Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders.
MeSH term(s)	Chromosomes, Human, X/genetics ; Developmental Disabilities/genetics ; Female ; Genes, Recessive ; Genes, X-Linked ; Genetic Diseases, X-Linked/genetics ; Genetic Variation ; Humans ; Inheritance Patterns/genetics ; Male ; Multifactorial Inheritance/genetics ; Mutation/genetics ; Phenotype ; Sex Characteristics
Language	English
Publishing date	2021-01-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-20852-3
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Article ; Online: Recontacting biobank participants to collect lifestyle, behavioural and cognitive information via online questionnaires: lessons from a pilot study within FinnGen.

Rodosthenous, Rodosthenis S / Niemi, Mari E K / Kallio, Lila / Perala, Merja / Terho, Perttu / Knopp, Theresa / Punkka, Eero / Makkonen, Enni M / Nurmi, Paula / Makela, Johanna / Wihuri, Pauli / Hautalahti, Marco / Moffatt, Corianna / Martini, Paolo / Germine, Laura / Makela, Viola A / Karhunen, Oona A / Lahti, Jari / Hiekkalinna, Tero S /

Jyrhama, Tero / Shen, Huei-Yi / Runz, Heiko / Palotie, Aarno / Perola, Markus / Ganna, Andrea

BMJ open

2022 Volume 12, Issue 10, Page(s) e064695

Abstract: Objectives: To recontact biobank participants and collect cognitive, behavioural and lifestyle information via a secure online platform.: Design: Biobank-based recontacting pilot study.: Setting: Three Finnish biobanks (Helsinki, Auria, Tampere) ... ...

Abstract	Objectives: To recontact biobank participants and collect cognitive, behavioural and lifestyle information via a secure online platform. Design: Biobank-based recontacting pilot study. Setting: Three Finnish biobanks (Helsinki, Auria, Tampere) recruiting participants from February 2021 to July 2021. Participants: All eligible invitees were enrolled in FinnGen by their biobanks (Helsinki, Auria, Tampere), had available genetic data and were >18 years old. Individuals with severe neuropsychiatric disease or cognitive or physical disabilities were excluded. Lastly, 5995 participants were selected based on their polygenic score for cognitive abilities and invited to the study. Among invitees, 1115 had successfully participated and completed the study questionnaire(s). Outcome measures: The primary outcome was the participation rate among study invitees. Secondary outcomes included questionnaire completion rate, quality of data collected and comparison of participation rate boosting strategies. Results: The overall participation rate was 18.6% among all invitees and 23.1% among individuals aged 18-69. A second reminder letter yielded an additional 9.7% participation rate in those who did not respond to the first invitation. Recontacting participants via an online healthcare portal yielded lower participation than recontacting via physical letter. The completion rate of the questionnaire and cognitive tests was high (92% and 85%, respectively), and measurements were overall reliable among participants. For example, the correlation (r) between self-reported body mass index and that collected by the biobanks was 0.92. Conclusion: In summary, this pilot suggests that recontacting FinnGen participants with the goal to collect a wide range of cognitive, behavioural and lifestyle information without additional engagement results in a low participation rate, but with reliable data. We suggest that such information be collected at enrolment, if possible, rather than via post hoc recontacting.
MeSH term(s)	Adolescent ; Biological Specimen Banks ; Cognition ; Duty to Recontact ; Humans ; Life Style ; Pilot Projects ; Surveys and Questionnaires
Language	English
Publishing date	2022-10-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2599832-8
ISSN	2044-6055 ; 2044-6055
ISSN (online)	2044-6055
ISSN	2044-6055
DOI	10.1136/bmjopen-2022-064695
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Article ; Online: The contribution of X-linked coding variation to severe developmental disorders

Hilary C. Martin / Eugene J. Gardner / Kaitlin E. Samocha / Joanna Kaplanis / Nadia Akawi / Alejandro Sifrim / Ruth Y. Eberhardt / Ana Lisa Taylor Tavares / Matthew D. C. Neville / Mari E. K. Niemi / Giuseppe Gallone / Jeremy McRae / Deciphering Developmental Disorders Study / Caroline F. Wright / David R. FitzPatrick / Helen V. Firth / Matthew E. Hurles

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 13

Abstract: Developmental disorders (DDs) are more prevalent in males, thought to be due to X-linked genetic variation. Here, the authors investigate the burden of X-linked coding variants in 11,044 DD patients, showing that this contributes to ~6% of both male and ... ...

Abstract	Developmental disorders (DDs) are more prevalent in males, thought to be due to X-linked genetic variation. Here, the authors investigate the burden of X-linked coding variants in 11,044 DD patients, showing that this contributes to ~6% of both male and female cases and therefore does not solely explain male bias in DDs.
Keywords	Science ; Q
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Genetic Architecture of Ischaemic Strokes after COVID-19 Shows Similarities with Large Vessel Strokes.

Llucià-Carol, Laia / Muiño, Elena / Cullell, Natalia / Cárcel-Márquez, Jara / Lledós, Miquel / Gallego-Fabrega, Cristina / Martin-Campos, Jesús / Martí-Fàbregas, Joan / Aguilera-Simón, Ana / Planas, Anna M / DeDiego, Marta L / de Felipe Mimbrera, Alicia / Masjuan, Jaime / García-Madrona, Sebastián / Segura, Tomás / González-Villar, Esther / Serrano-Heras, Gemma / Domínguez Mayoral, Ana / Menéndez-Valladares, Paloma /

Montaner, Joan / Migeotte, Isabelle / Rahmouni, Souad / Darcis, Gilles / Bernardo, David / Rojo, Silvia / Schulte, Eva C / Protzer, Ulrike / Fricke, Lisa / Winter, Christof / Niemi, Mari E K / Cordioli, Mattia / Delgado, Pilar / Fernández-Cadenas, Israel

International journal of molecular sciences

2023 Volume 24, Issue 17

Abstract: We aimed to analyse whether patients with ischaemic stroke (IS) occurring within eight days after the onset of COVID-19 (IS-COV) are associated with a specific aetiology of IS. We used SUPERGNOVA to identify genome regions that correlate between the IS- ... ...

Abstract	We aimed to analyse whether patients with ischaemic stroke (IS) occurring within eight days after the onset of COVID-19 (IS-COV) are associated with a specific aetiology of IS. We used SUPERGNOVA to identify genome regions that correlate between the IS-COV cohort (73 IS-COV cases vs. 701 population controls) and different aetiological subtypes. Polygenic risk scores (PRSs) for each subtype were generated and tested in the IS-COV cohort using PRSice-2 and PLINK to find genetic associations. Both analyses used the IS-COV cohort and GWAS from MEGASTROKE (67,162 stroke patients vs. 454,450 population controls), GIGASTROKE (110,182 vs. 1,503,898), and the NINDS Stroke Genetics Network (16,851 vs. 32,473). Three genomic regions were associated (
MeSH term(s)	Humans ; Stroke/complications ; Stroke/genetics ; Brain Ischemia/complications ; Brain Ischemia/genetics ; COVID-19/complications ; COVID-19/genetics ; Ischemic Stroke/genetics ; Arteries ; Embolic Stroke ; Atherosclerosis
Language	English
Publishing date	2023-08-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241713452
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Article ; Online: Author Correction: FinnGen provides genetic insights from a well-phenotyped isolated population.

Kurki, Mitja I / Karjalainen, Juha / Palta, Priit / Sipilä, Timo P / Kristiansson, Kati / Donner, Kati M / Reeve, Mary P / Laivuori, Hannele / Aavikko, Mervi / Kaunisto, Mari A / Loukola, Anu / Lahtela, Elisa / Mattsson, Hannele / Laiho, Päivi / Della Briotta Parolo, Pietro / Lehisto, Arto A / Kanai, Masahiro / Mars, Nina / Rämö, Joel /

Kiiskinen, Tuomo / Heyne, Henrike O / Veerapen, Kumar / Rüeger, Sina / Lemmelä, Susanna / Zhou, Wei / Ruotsalainen, Sanni / Pärn, Kalle / Hiekkalinna, Tero / Koskelainen, Sami / Paajanen, Teemu / Llorens, Vincent / Gracia-Tabuenca, Javier / Siirtola, Harri / Reis, Kadri / Elnahas, Abdelrahman G / Sun, Benjamin / Foley, Christopher N / Aalto-Setälä, Katriina / Alasoo, Kaur / Arvas, Mikko / Auro, Kirsi / Biswas, Shameek / Bizaki-Vallaskangas, Argyro / Carpen, Olli / Chen, Chia-Yen / Dada, Oluwaseun A / Ding, Zhihao / Ehm, Margaret G / Eklund, Kari / Färkkilä, Martti / Finucane, Hilary / Ganna, Andrea / Ghazal, Awaisa / Graham, Robert R / Green, Eric M / Hakanen, Antti / Hautalahti, Marco / Hedman, Åsa K / Hiltunen, Mikko / Hinttala, Reetta / Hovatta, Iiris / Hu, Xinli / Huertas-Vazquez, Adriana / Huilaja, Laura / Hunkapiller, Julie / Jacob, Howard / Jensen, Jan-Nygaard / Joensuu, Heikki / John, Sally / Julkunen, Valtteri / Jung, Marc / Junttila, Juhani / Kaarniranta, Kai / Kähönen, Mika / Kajanne, Risto / Kallio, Lila / Kälviäinen, Reetta / Kaprio, Jaakko / Kerimov, Nurlan / Kettunen, Johannes / Kilpeläinen, Elina / Kilpi, Terhi / Klinger, Katherine / Kosma, Veli-Matti / Kuopio, Teijo / Kurra, Venla / Laisk, Triin / Laukkanen, Jari / Lawless, Nathan / Liu, Aoxing / Longerich, Simonne / Mägi, Reedik / Mäkelä, Johanna / Mäkitie, Antti / Malarstig, Anders / Mannermaa, Arto / Maranville, Joseph / Matakidou, Athena / Meretoja, Tuomo / Mozaffari, Sahar V / Niemi, Mari E K / Niemi, Marianna / Niiranen, Teemu / O Donnell, Christopher J / Obeidat, Ma En / Okafo, George / Ollila, Hanna M / Palomäki, Antti / Palotie, Tuula / Partanen, Jukka / Paul, Dirk S / Pelkonen, Margit / Pendergrass, Rion K / Petrovski, Slavé / Pitkäranta, Anne / Platt, Adam / Pulford, David / Punkka, Eero / Pussinen, Pirkko / Raghavan, Neha / Rahimov, Fedik / Rajpal, Deepak / Renaud, Nicole A / Riley-Gillis, Bridget / Rodosthenous, Rodosthenis / Saarentaus, Elmo / Salminen, Aino / Salminen, Eveliina / Salomaa, Veikko / Schleutker, Johanna / Serpi, Raisa / Shen, Huei-Yi / Siegel, Richard / Silander, Kaisa / Siltanen, Sanna / Soini, Sirpa / Soininen, Hilkka / Sul, Jae Hoon / Tachmazidou, Ioanna / Tasanen, Kaisa / Tienari, Pentti / Toppila-Salmi, Sanna / Tukiainen, Taru / Tuomi, Tiinamaija / Turunen, Joni A / Ulirsch, Jacob C / Vaura, Felix / Virolainen, Petri / Waring, Jeffrey / Waterworth, Dawn / Yang, Robert / Nelis, Mari / Reigo, Anu / Metspalu, Andres / Milani, Lili / Esko, Tõnu / Fox, Caroline / Havulinna, Aki S / Perola, Markus / Ripatti, Samuli / Jalanko, Anu / Laitinen, Tarja / Mäkelä, Tomi P / Plenge, Robert / McCarthy, Mark / Runz, Heiko / Daly, Mark J / Palotie, Aarno

Nature

2023 Volume 615, Issue 7952, Page(s) E19

Language	English
Publishing date	2023-02-24
Publishing country	England
Document type	Published Erratum
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-05837-8
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Article ; Online: FinnGen provides genetic insights from a well-phenotyped isolated population.

Nature

2023 Volume 613, Issue 7944, Page(s) 508–518

Abstract: Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck ... ...

Abstract	Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored
MeSH term(s)	Humans ; Middle Aged ; Disease/genetics ; Estonia ; Finland ; Gene Frequency/genetics ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Meta-Analysis as Topic ; Phenotype ; United Kingdom ; White People/genetics
Language	English
Publishing date	2023-01-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-022-05473-8
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Article ; Online: Common genetic variants contribute to risk of rare severe neurodevelopmental disorders.

Niemi, Mari E K / Martin, Hilary C / Rice, Daniel L / Gallone, Giuseppe / Gordon, Scott / Kelemen, Martin / McAloney, Kerrie / McRae, Jeremy / Radford, Elizabeth J / Yu, Sui / Gecz, Jozef / Martin, Nicholas G / Wright, Caroline F / Fitzpatrick, David R / Firth, Helen V / Hurles, Matthew E / Barrett, Jeffrey C

Nature

2018 Volume 562, Issue 7726, Page(s) 268–271

Abstract: There are thousands of rare human disorders that are caused by single deleterious, protein-coding genetic ... ...

Abstract	There are thousands of rare human disorders that are caused by single deleterious, protein-coding genetic variants
MeSH term(s)	Autistic Disorder/genetics ; Birth Weight/genetics ; Body Height/genetics ; Case-Control Studies ; Cohort Studies ; Developmental Disabilities/genetics ; Female ; Genetic Predisposition to Disease ; Genetic Variation ; Genome-Wide Association Study ; Humans ; Intelligence/genetics ; Linkage Disequilibrium ; Male ; Multifactorial Inheritance/genetics ; Neurodevelopmental Disorders/genetics ; Phenotype ; Rare Diseases/genetics ; Schizophrenia/genetics
Language	English
Publishing date	2018-09-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-018-0566-4
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