Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study
<h3>Background</h3><p dir="ltr">Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills, restricted interests, and repetitive behaviors. The prevalence of ASD among children in Qatar was recently estimated...
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2023
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| _version_ | 1864513507209248768 |
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| author | Mona Abdi (10196665) |
| author2 | Elbay Aliyev (14056972) Brett Trost (140006) Muhammad Kohailan (748774) Waleed Aamer (14056969) Najeeb Syed (12561967) Rulan Shaath (17112852) Geethanjali Devadoss Gandhi (14056966) Worrawat Engchuan (9377702) Jennifer Howe (625602) Bhooma Thiruvahindrapuram (143687) Melissa Geng (17112855) Joe Whitney (58034) Amira Syed (17112858) Jyothi Lakshmi (17112861) Sura Hussein (14152557) Najwa Albashir (17112864) Amal Hussein (7956473) Ilaria Poggiolini (296742) Saba F. Elhag (17112867) Sasirekha Palaniswamy (14152563) Marios Kambouris (3441308) Maria de Fatima Janjua (17112870) Mohamed O. El Tahir (17112873) Ahsan Nazeer (17112876) Durre Shahwar (613605) Muhammad Waqar Azeem (11909633) Younes Mokrab (6367) Nazim Abdel Aati (17112879) Ammira Akil (17112882) Stephen W. Scherer (7434836) Madeeha Kamal (16535217) Khalid A. Fakhro (3158862) |
| author2_role | author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| author_facet | Mona Abdi (10196665) Elbay Aliyev (14056972) Brett Trost (140006) Muhammad Kohailan (748774) Waleed Aamer (14056969) Najeeb Syed (12561967) Rulan Shaath (17112852) Geethanjali Devadoss Gandhi (14056966) Worrawat Engchuan (9377702) Jennifer Howe (625602) Bhooma Thiruvahindrapuram (143687) Melissa Geng (17112855) Joe Whitney (58034) Amira Syed (17112858) Jyothi Lakshmi (17112861) Sura Hussein (14152557) Najwa Albashir (17112864) Amal Hussein (7956473) Ilaria Poggiolini (296742) Saba F. Elhag (17112867) Sasirekha Palaniswamy (14152563) Marios Kambouris (3441308) Maria de Fatima Janjua (17112870) Mohamed O. El Tahir (17112873) Ahsan Nazeer (17112876) Durre Shahwar (613605) Muhammad Waqar Azeem (11909633) Younes Mokrab (6367) Nazim Abdel Aati (17112879) Ammira Akil (17112882) Stephen W. Scherer (7434836) Madeeha Kamal (16535217) Khalid A. Fakhro (3158862) |
| author_role | author |
| dc.creator.none.fl_str_mv | Mona Abdi (10196665) Elbay Aliyev (14056972) Brett Trost (140006) Muhammad Kohailan (748774) Waleed Aamer (14056969) Najeeb Syed (12561967) Rulan Shaath (17112852) Geethanjali Devadoss Gandhi (14056966) Worrawat Engchuan (9377702) Jennifer Howe (625602) Bhooma Thiruvahindrapuram (143687) Melissa Geng (17112855) Joe Whitney (58034) Amira Syed (17112858) Jyothi Lakshmi (17112861) Sura Hussein (14152557) Najwa Albashir (17112864) Amal Hussein (7956473) Ilaria Poggiolini (296742) Saba F. Elhag (17112867) Sasirekha Palaniswamy (14152563) Marios Kambouris (3441308) Maria de Fatima Janjua (17112870) Mohamed O. El Tahir (17112873) Ahsan Nazeer (17112876) Durre Shahwar (613605) Muhammad Waqar Azeem (11909633) Younes Mokrab (6367) Nazim Abdel Aati (17112879) Ammira Akil (17112882) Stephen W. Scherer (7434836) Madeeha Kamal (16535217) Khalid A. Fakhro (3158862) |
| dc.date.none.fl_str_mv | 2023-10-07T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1186/s13073-023-01228-w |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Genomic_architecture_of_autism_spectrum_disorder_in_Qatar_The_BARAKA-Qatar_Study/26808628 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Neurosciences Health sciences Public health De novo variants Whole genome sequencing SNVs Middle Eastern population Autism spectrum disorder ASD BARAKA cohort ASD risk genes |
| dc.title.none.fl_str_mv | Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <h3>Background</h3><p dir="ltr">Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills, restricted interests, and repetitive behaviors. The prevalence of ASD among children in Qatar was recently estimated to be 1.1%, though the genetic architecture underlying ASD both in Qatar and the greater Middle East has been largely unexplored. Here, we describe the first genomic data release from the BARAKA-Qatar Study—a nationwide program building a broadly consented biorepository of individuals with ASD and their families available for sample and data sharing and multi-omics research.</p><h3>Methods</h3><p dir="ltr">In this first release, we present a comprehensive analysis of whole-genome sequencing (WGS) data of the first 100 families (372 individuals), investigating the genetic architecture, including single-nucleotide variants (SNVs), copy number variants (CNVs), tandem repeat expansions (TREs), as well as mitochondrial DNA variants (mtDNA) segregating with ASD in local families.</p><h3>Results</h3><p dir="ltr">Overall, we identify potentially pathogenic variants in known genes or regions in 27 out of 100 families (27%), of which 11 variants (40.7%) were classified as pathogenic or likely-pathogenic based on American College of Medical Genetics (ACMG) guidelines. Dominant variants, including de novo and inherited, contributed to 15 (55.6%) of these families, consisting of SNVs/indels (66.7%), CNVs (13.3%), TREs (13.3%), and mtDNA variants (6.7%). Moreover, homozygous variants were found in 7 families (25.9%), with a sixfold increase in homozygous burden in consanguineous versus non-consanguineous families (13.6% and 1.8%, respectively). Furthermore, 28 novel ASD candidate genes were identified in 20 families, 23 of which had recurrent hits in MSSNG and SSC cohorts.</p><h3>Conclusions</h3><p dir="ltr">This study illustrates the value of ASD studies in under-represented populations and the importance of WGS as a comprehensive tool for establishing a molecular diagnosis for families with ASD. Moreover, it uncovers a significant role for recessive variation in ASD architecture in consanguineous settings and provides a unique resource of Middle Eastern genomes for future research to the global ASD community.</p><h2>Other Information</h2><p dir="ltr">Published in: Genome Medicine<br>License: <a href="https://creativecommons.org/licenses/by/4.0" target="_blank">https://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1186/s13073-023-01228-w" target="_blank">https://dx.doi.org/10.1186/s13073-023-01228-w</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_cc8c1962ed976a27a32bf0f01b665995 |
| identifier_str_mv | 10.1186/s13073-023-01228-w |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/26808628 |
| publishDate | 2023 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar StudyMona Abdi (10196665)Elbay Aliyev (14056972)Brett Trost (140006)Muhammad Kohailan (748774)Waleed Aamer (14056969)Najeeb Syed (12561967)Rulan Shaath (17112852)Geethanjali Devadoss Gandhi (14056966)Worrawat Engchuan (9377702)Jennifer Howe (625602)Bhooma Thiruvahindrapuram (143687)Melissa Geng (17112855)Joe Whitney (58034)Amira Syed (17112858)Jyothi Lakshmi (17112861)Sura Hussein (14152557)Najwa Albashir (17112864)Amal Hussein (7956473)Ilaria Poggiolini (296742)Saba F. Elhag (17112867)Sasirekha Palaniswamy (14152563)Marios Kambouris (3441308)Maria de Fatima Janjua (17112870)Mohamed O. El Tahir (17112873)Ahsan Nazeer (17112876)Durre Shahwar (613605)Muhammad Waqar Azeem (11909633)Younes Mokrab (6367)Nazim Abdel Aati (17112879)Ammira Akil (17112882)Stephen W. Scherer (7434836)Madeeha Kamal (16535217)Khalid A. Fakhro (3158862)Biological sciencesGeneticsBiomedical and clinical sciencesClinical sciencesNeurosciencesHealth sciencesPublic healthDe novo variantsWhole genome sequencingSNVsMiddle Eastern populationAutism spectrum disorderASDBARAKA cohortASD risk genes<h3>Background</h3><p dir="ltr">Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills, restricted interests, and repetitive behaviors. The prevalence of ASD among children in Qatar was recently estimated to be 1.1%, though the genetic architecture underlying ASD both in Qatar and the greater Middle East has been largely unexplored. Here, we describe the first genomic data release from the BARAKA-Qatar Study—a nationwide program building a broadly consented biorepository of individuals with ASD and their families available for sample and data sharing and multi-omics research.</p><h3>Methods</h3><p dir="ltr">In this first release, we present a comprehensive analysis of whole-genome sequencing (WGS) data of the first 100 families (372 individuals), investigating the genetic architecture, including single-nucleotide variants (SNVs), copy number variants (CNVs), tandem repeat expansions (TREs), as well as mitochondrial DNA variants (mtDNA) segregating with ASD in local families.</p><h3>Results</h3><p dir="ltr">Overall, we identify potentially pathogenic variants in known genes or regions in 27 out of 100 families (27%), of which 11 variants (40.7%) were classified as pathogenic or likely-pathogenic based on American College of Medical Genetics (ACMG) guidelines. Dominant variants, including de novo and inherited, contributed to 15 (55.6%) of these families, consisting of SNVs/indels (66.7%), CNVs (13.3%), TREs (13.3%), and mtDNA variants (6.7%). Moreover, homozygous variants were found in 7 families (25.9%), with a sixfold increase in homozygous burden in consanguineous versus non-consanguineous families (13.6% and 1.8%, respectively). Furthermore, 28 novel ASD candidate genes were identified in 20 families, 23 of which had recurrent hits in MSSNG and SSC cohorts.</p><h3>Conclusions</h3><p dir="ltr">This study illustrates the value of ASD studies in under-represented populations and the importance of WGS as a comprehensive tool for establishing a molecular diagnosis for families with ASD. Moreover, it uncovers a significant role for recessive variation in ASD architecture in consanguineous settings and provides a unique resource of Middle Eastern genomes for future research to the global ASD community.</p><h2>Other Information</h2><p dir="ltr">Published in: Genome Medicine<br>License: <a href="https://creativecommons.org/licenses/by/4.0" target="_blank">https://creativecommons.org/licenses/by/4.0</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1186/s13073-023-01228-w" target="_blank">https://dx.doi.org/10.1186/s13073-023-01228-w</a></p>2023-10-07T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1186/s13073-023-01228-whttps://figshare.com/articles/journal_contribution/Genomic_architecture_of_autism_spectrum_disorder_in_Qatar_The_BARAKA-Qatar_Study/26808628CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/268086282023-10-07T03:00:00Z |
| spellingShingle | Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study Mona Abdi (10196665) Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Neurosciences Health sciences Public health De novo variants Whole genome sequencing SNVs Middle Eastern population Autism spectrum disorder ASD BARAKA cohort ASD risk genes |
| status_str | publishedVersion |
| title | Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study |
| title_full | Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study |
| title_fullStr | Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study |
| title_full_unstemmed | Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study |
| title_short | Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study |
| title_sort | Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study |
| topic | Biological sciences Genetics Biomedical and clinical sciences Clinical sciences Neurosciences Health sciences Public health De novo variants Whole genome sequencing SNVs Middle Eastern population Autism spectrum disorder ASD BARAKA cohort ASD risk genes |