Extended haplotype with rs41524547-G defines the ancestral origin of SCA10
Abstract Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal dominant ataxia caused by a large expansion of the (ATTCT)n repeat in ATXN10. SCA10 was described in Native American and Asian individuals which prompted a search for an expanded haplotype to confirm a common ancestral origin for th...
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creator | McFarland, Karen N Tiwari, Anjana Hashem, Vera Zhang, Linwei Zeng, Desmond Vincent, Justin Arredondo, Maria J Johnson, Kristy L Gan, Shi Rui Yabe, Ichiro Skov, Laurits Rasmussen, Astrid Ashizawa, Tetsuo |
description | Abstract
Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal dominant ataxia caused by a large expansion of the (ATTCT)n repeat in ATXN10. SCA10 was described in Native American and Asian individuals which prompted a search for an expanded haplotype to confirm a common ancestral origin for the expansion event. All patients with SCA10 expansions in our cohort share a single haplotype defined at the 5′-end by the minor allele of rs41524547, located ~35 kb upstream of the SCA10 expansion. Intriguingly, rs41524547 is located within the miRNA gene, MIR4762, within its DROSHA cleavage site and just outside the seed sequence for mir4792-5p. The world-wide frequency of rs41524547-G is less than 5% and found almost exclusively in the Americas and East Asia—a geographic distribution that mirrors reported SCA10 cases. We identified rs41524547-G(+) DNA from the 1000 Genomes/International Genome Sample Resource and our own general population samples and identified SCA10 repeat expansions in up to 25% of these samples. The reduced penetrance of these SCA10 expansions may be explained by a young (pre-onset) age at sample collection, a small repeat size, purity of repeat units, or the disruption of miR4762-5p function. We conclude that rs41524547-G is the most robust at-risk SNP allele for SCA10, is useful for screening of SCA10 expansions in population genetics studies and provides the most compelling evidence to date for a single, prehistoric origin of SCA10 expansions sometime prior to or during the migration of individuals across the Bering Land Bridge into the Americas. |
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Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal dominant ataxia caused by a large expansion of the (ATTCT)n repeat in ATXN10. SCA10 was described in Native American and Asian individuals which prompted a search for an expanded haplotype to confirm a common ancestral origin for the expansion event. All patients with SCA10 expansions in our cohort share a single haplotype defined at the 5′-end by the minor allele of rs41524547, located ~35 kb upstream of the SCA10 expansion. Intriguingly, rs41524547 is located within the miRNA gene, MIR4762, within its DROSHA cleavage site and just outside the seed sequence for mir4792-5p. The world-wide frequency of rs41524547-G is less than 5% and found almost exclusively in the Americas and East Asia—a geographic distribution that mirrors reported SCA10 cases. We identified rs41524547-G(+) DNA from the 1000 Genomes/International Genome Sample Resource and our own general population samples and identified SCA10 repeat expansions in up to 25% of these samples. The reduced penetrance of these SCA10 expansions may be explained by a young (pre-onset) age at sample collection, a small repeat size, purity of repeat units, or the disruption of miR4762-5p function. We conclude that rs41524547-G is the most robust at-risk SNP allele for SCA10, is useful for screening of SCA10 expansions in population genetics studies and provides the most compelling evidence to date for a single, prehistoric origin of SCA10 expansions sometime prior to or during the migration of individuals across the Bering Land Bridge into the Americas.</description><identifier>ISSN: 0964-6906</identifier><identifier>ISSN: 1460-2083</identifier><identifier>EISSN: 1460-2083</identifier><identifier>DOI: 10.1093/hmg/ddae092</identifier><identifier>PMID: 38832639</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Alleles ; Ataxin-10 - genetics ; DNA Repeat Expansion ; Gene Frequency ; Haplotypes - genetics ; Humans ; MicroRNAs - genetics ; Nerve Tissue Proteins - genetics ; Polymorphism, Single Nucleotide - genetics ; Spinocerebellar Ataxias - genetics</subject><ispartof>Human molecular genetics, 2024-09, Vol.33 (18), p.1567-1574</ispartof><rights>The Author(s) 2024. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2024</rights><rights>The Author(s) 2024. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c1239-4c68103878d62ef40437f4d1951f914789679b6d57d4d11eab857659162392f43</cites><orcidid>0000-0002-9952-8678</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,781,785,27929,27930</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38832639$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>McFarland, Karen N</creatorcontrib><creatorcontrib>Tiwari, Anjana</creatorcontrib><creatorcontrib>Hashem, Vera</creatorcontrib><creatorcontrib>Zhang, Linwei</creatorcontrib><creatorcontrib>Zeng, Desmond</creatorcontrib><creatorcontrib>Vincent, Justin</creatorcontrib><creatorcontrib>Arredondo, Maria J</creatorcontrib><creatorcontrib>Johnson, Kristy L</creatorcontrib><creatorcontrib>Gan, Shi Rui</creatorcontrib><creatorcontrib>Yabe, Ichiro</creatorcontrib><creatorcontrib>Skov, Laurits</creatorcontrib><creatorcontrib>Rasmussen, Astrid</creatorcontrib><creatorcontrib>Ashizawa, Tetsuo</creatorcontrib><title>Extended haplotype with rs41524547-G defines the ancestral origin of SCA10</title><title>Human molecular genetics</title><addtitle>Hum Mol Genet</addtitle><description>Abstract
Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal dominant ataxia caused by a large expansion of the (ATTCT)n repeat in ATXN10. SCA10 was described in Native American and Asian individuals which prompted a search for an expanded haplotype to confirm a common ancestral origin for the expansion event. All patients with SCA10 expansions in our cohort share a single haplotype defined at the 5′-end by the minor allele of rs41524547, located ~35 kb upstream of the SCA10 expansion. Intriguingly, rs41524547 is located within the miRNA gene, MIR4762, within its DROSHA cleavage site and just outside the seed sequence for mir4792-5p. The world-wide frequency of rs41524547-G is less than 5% and found almost exclusively in the Americas and East Asia—a geographic distribution that mirrors reported SCA10 cases. We identified rs41524547-G(+) DNA from the 1000 Genomes/International Genome Sample Resource and our own general population samples and identified SCA10 repeat expansions in up to 25% of these samples. The reduced penetrance of these SCA10 expansions may be explained by a young (pre-onset) age at sample collection, a small repeat size, purity of repeat units, or the disruption of miR4762-5p function. We conclude that rs41524547-G is the most robust at-risk SNP allele for SCA10, is useful for screening of SCA10 expansions in population genetics studies and provides the most compelling evidence to date for a single, prehistoric origin of SCA10 expansions sometime prior to or during the migration of individuals across the Bering Land Bridge into the Americas.</description><subject>Alleles</subject><subject>Ataxin-10 - genetics</subject><subject>DNA Repeat Expansion</subject><subject>Gene Frequency</subject><subject>Haplotypes - genetics</subject><subject>Humans</subject><subject>MicroRNAs - genetics</subject><subject>Nerve Tissue Proteins - genetics</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Spinocerebellar Ataxias - genetics</subject><issn>0964-6906</issn><issn>1460-2083</issn><issn>1460-2083</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kM9LwzAYhoMobk5P3iUnEaQuadI0OY4ypzLwoJ5L1nxZK_1l0qL7741sevT0wcfzvrw8CF1SckeJYvOy2c6N0UBUfISmlAsSxUSyYzQlSvBIKCIm6Mz7d0Ko4Cw9RRMmJYsFU1P0tPwaoDVgcKn7uht2PeDPaiix85wmMU94Gq2wAVu14PFQAtZtAX5wusadq7ZVizuLX7IFJefoxOraw8XhztDb_fI1e4jWz6vHbLGOChozFfFCSEqYTKURMVhOwiTLDVUJtYryVCqRqo0wSWrCl4LeyCQViaIipGPL2Qzd7Ht7132MYUveVL6AutYtdKPPGRE8kWG6DOjtHi1c570Dm_euarTb5ZTkP_LyIC8_yAv01aF43DRg_thfWwG43gPd2P_b9A3bCXQk</recordid><startdate>20240903</startdate><enddate>20240903</enddate><creator>McFarland, Karen N</creator><creator>Tiwari, Anjana</creator><creator>Hashem, Vera</creator><creator>Zhang, Linwei</creator><creator>Zeng, Desmond</creator><creator>Vincent, Justin</creator><creator>Arredondo, Maria J</creator><creator>Johnson, Kristy L</creator><creator>Gan, Shi Rui</creator><creator>Yabe, Ichiro</creator><creator>Skov, Laurits</creator><creator>Rasmussen, Astrid</creator><creator>Ashizawa, Tetsuo</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-9952-8678</orcidid></search><sort><creationdate>20240903</creationdate><title>Extended haplotype with rs41524547-G defines the ancestral origin of SCA10</title><author>McFarland, Karen N ; Tiwari, Anjana ; Hashem, Vera ; Zhang, Linwei ; Zeng, Desmond ; Vincent, Justin ; Arredondo, Maria J ; Johnson, Kristy L ; Gan, Shi Rui ; Yabe, Ichiro ; Skov, Laurits ; Rasmussen, Astrid ; Ashizawa, Tetsuo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c1239-4c68103878d62ef40437f4d1951f914789679b6d57d4d11eab857659162392f43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Alleles</topic><topic>Ataxin-10 - genetics</topic><topic>DNA Repeat Expansion</topic><topic>Gene Frequency</topic><topic>Haplotypes - genetics</topic><topic>Humans</topic><topic>MicroRNAs - genetics</topic><topic>Nerve Tissue Proteins - genetics</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Spinocerebellar Ataxias - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>McFarland, Karen N</creatorcontrib><creatorcontrib>Tiwari, Anjana</creatorcontrib><creatorcontrib>Hashem, Vera</creatorcontrib><creatorcontrib>Zhang, Linwei</creatorcontrib><creatorcontrib>Zeng, Desmond</creatorcontrib><creatorcontrib>Vincent, Justin</creatorcontrib><creatorcontrib>Arredondo, Maria J</creatorcontrib><creatorcontrib>Johnson, Kristy L</creatorcontrib><creatorcontrib>Gan, Shi Rui</creatorcontrib><creatorcontrib>Yabe, Ichiro</creatorcontrib><creatorcontrib>Skov, Laurits</creatorcontrib><creatorcontrib>Rasmussen, Astrid</creatorcontrib><creatorcontrib>Ashizawa, Tetsuo</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Human molecular genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>McFarland, Karen N</au><au>Tiwari, Anjana</au><au>Hashem, Vera</au><au>Zhang, Linwei</au><au>Zeng, Desmond</au><au>Vincent, Justin</au><au>Arredondo, Maria J</au><au>Johnson, Kristy L</au><au>Gan, Shi Rui</au><au>Yabe, Ichiro</au><au>Skov, Laurits</au><au>Rasmussen, Astrid</au><au>Ashizawa, Tetsuo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Extended haplotype with rs41524547-G defines the ancestral origin of SCA10</atitle><jtitle>Human molecular genetics</jtitle><addtitle>Hum Mol Genet</addtitle><date>2024-09-03</date><risdate>2024</risdate><volume>33</volume><issue>18</issue><spage>1567</spage><epage>1574</epage><pages>1567-1574</pages><issn>0964-6906</issn><issn>1460-2083</issn><eissn>1460-2083</eissn><abstract>Abstract
Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal dominant ataxia caused by a large expansion of the (ATTCT)n repeat in ATXN10. SCA10 was described in Native American and Asian individuals which prompted a search for an expanded haplotype to confirm a common ancestral origin for the expansion event. All patients with SCA10 expansions in our cohort share a single haplotype defined at the 5′-end by the minor allele of rs41524547, located ~35 kb upstream of the SCA10 expansion. Intriguingly, rs41524547 is located within the miRNA gene, MIR4762, within its DROSHA cleavage site and just outside the seed sequence for mir4792-5p. The world-wide frequency of rs41524547-G is less than 5% and found almost exclusively in the Americas and East Asia—a geographic distribution that mirrors reported SCA10 cases. We identified rs41524547-G(+) DNA from the 1000 Genomes/International Genome Sample Resource and our own general population samples and identified SCA10 repeat expansions in up to 25% of these samples. The reduced penetrance of these SCA10 expansions may be explained by a young (pre-onset) age at sample collection, a small repeat size, purity of repeat units, or the disruption of miR4762-5p function. We conclude that rs41524547-G is the most robust at-risk SNP allele for SCA10, is useful for screening of SCA10 expansions in population genetics studies and provides the most compelling evidence to date for a single, prehistoric origin of SCA10 expansions sometime prior to or during the migration of individuals across the Bering Land Bridge into the Americas.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>38832639</pmid><doi>10.1093/hmg/ddae092</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0002-9952-8678</orcidid></addata></record> |
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subjects | Alleles Ataxin-10 - genetics DNA Repeat Expansion Gene Frequency Haplotypes - genetics Humans MicroRNAs - genetics Nerve Tissue Proteins - genetics Polymorphism, Single Nucleotide - genetics Spinocerebellar Ataxias - genetics |
title | Extended haplotype with rs41524547-G defines the ancestral origin of SCA10 |
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