Loading…
Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR‐mediated deletion and characterization of 4 nonsynonymous single‐nucleotide polymorphisms
BACKGROUND The human FUT2 gene, which encodes a secretor type α(1,2)fucosyltransferase, is reported to have several population‐specific single‐nucleotide polymorphisms (SNPs) and copy number variations. However, little is known about genetic variation of FUT2 in Native Americans. STUDY DESIGN AND ME...
Saved in:
| Published in: | Transfusion (Philadelphia, Pa.) Pa.), 2019-07, Vol.59 (7), p.2415-2421 |
|---|---|
| Main Authors: | , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that this one cites Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-c4198-c994c8eb884e8d194deebddd75d59e8ff864a3142068df29cb3c9d8dbc48fe023 |
|---|---|
| cites | cdi_FETCH-LOGICAL-c4198-c994c8eb884e8d194deebddd75d59e8ff864a3142068df29cb3c9d8dbc48fe023 |
| container_end_page | 2421 |
| container_issue | 7 |
| container_start_page | 2415 |
| container_title | Transfusion (Philadelphia, Pa.) |
| container_volume | 59 |
| creator | Soejima, Mikiko Koda, Yoshiro |
| description | BACKGROUND
The human FUT2 gene, which encodes a secretor type α(1,2)fucosyltransferase, is reported to have several population‐specific single‐nucleotide polymorphisms (SNPs) and copy number variations. However, little is known about genetic variation of FUT2 in Native Americans.
STUDY DESIGN AND METHODS
To detect SNPs and copy number variations of the FUT2 gene in Peruvians, direct sequencing and digital polymerase chain reaction were performed. Haplotypes of observed SNPs were estimated by PHASE software or cloning into plasmids. The functional significance of nonsynonymous SNPs was examined by transient transfection assay.
RESULTS
We identified three novel nonfunctional alleles (se178,357, se841, and sedel4) due to two nonsynonymous SNPs (178C > T and 841G > A) and a novel long terminal repeat–mediated recombination with a 4.3‐kb deletion in 70 Peruvians. The frequency of nonfunctional alleles was relative low (20.7%). Because se841 has a relatively high frequency (5.7%), it might be a suitable genetic marker for Peruvians.
CONCLUSION
We identified three novel nonfunctional alleles in 70 Peruvians. To our knowledge, this is the first time a long terminal repeat–mediated gene recombination event at the FUT2 locus has been detected. |
| doi_str_mv | 10.1111/trf.15298 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_journals_2251104222</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2251104222</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4198-c994c8eb884e8d194deebddd75d59e8ff864a3142068df29cb3c9d8dbc48fe023</originalsourceid><addsrcrecordid>eNp1kUFOGzEUhi1URALtoheoLHXVxRDb4yF2dxVqKFIkEErWI4_9XBxN7Kk9ExRWHKE36Z04SU0C2eGFvfD3vl96P0KfKTmn-Uz6aM9pxaQ4QmNaldOCSVl9QGNCOC0oLdkInaa0IoQwSegJGpVEVlPGxRj9uwIPvdN4o6JTvQseB4tnywXDzmOFbyEOG6c87kI3tDvgO3YGfO-s04cBhX3YQIvni7vnp79rMNkFBhtoYYcob7C-V1HpHqJ7PMzxPOfTNl_bdRgSTs7_biEr_KBbCH1Oyslt_ozdvUvr9BEdW9Um-PT6nqHl7Ofi8lcxv7m6vvwxLzSnUhRaSq4FNEJwEIZKbgAaY8y0MpUEYa244KqknJELYSyTuim1NMI0mgsLhJVn6Ove28XwZ4DU16swRJ8ja8YqSgln7IX6tqd0DClFsHUX3VrFbU1J_VJNnaupd9Vk9surcWjygg7kWxcZmOyBB9fC9n1Tvbib7ZX_ASEZnxg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2251104222</pqid></control><display><type>article</type><title>Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR‐mediated deletion and characterization of 4 nonsynonymous single‐nucleotide polymorphisms</title><source>Wiley-Blackwell Read & Publish Collection</source><creator>Soejima, Mikiko ; Koda, Yoshiro</creator><creatorcontrib>Soejima, Mikiko ; Koda, Yoshiro</creatorcontrib><description>BACKGROUND
The human FUT2 gene, which encodes a secretor type α(1,2)fucosyltransferase, is reported to have several population‐specific single‐nucleotide polymorphisms (SNPs) and copy number variations. However, little is known about genetic variation of FUT2 in Native Americans.
STUDY DESIGN AND METHODS
To detect SNPs and copy number variations of the FUT2 gene in Peruvians, direct sequencing and digital polymerase chain reaction were performed. Haplotypes of observed SNPs were estimated by PHASE software or cloning into plasmids. The functional significance of nonsynonymous SNPs was examined by transient transfection assay.
RESULTS
We identified three novel nonfunctional alleles (se178,357, se841, and sedel4) due to two nonsynonymous SNPs (178C > T and 841G > A) and a novel long terminal repeat–mediated recombination with a 4.3‐kb deletion in 70 Peruvians. The frequency of nonfunctional alleles was relative low (20.7%). Because se841 has a relatively high frequency (5.7%), it might be a suitable genetic marker for Peruvians.
CONCLUSION
We identified three novel nonfunctional alleles in 70 Peruvians. To our knowledge, this is the first time a long terminal repeat–mediated gene recombination event at the FUT2 locus has been detected.</description><identifier>ISSN: 0041-1132</identifier><identifier>EISSN: 1537-2995</identifier><identifier>DOI: 10.1111/trf.15298</identifier><identifier>PMID: 30957248</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>Alleles ; Base Sequence ; Clonal deletion ; Cloning ; Copy number ; DNA Copy Number Variations ; Female ; Fucosyltransferases - genetics ; FUT2 gene ; Galactoside 2-alpha-L-fucosyltransferase ; Gene deletion ; Gene Frequency ; Gene sequencing ; Genetic diversity ; Genetic markers ; Haplotypes ; Humans ; Indians, South American - genetics ; Long terminal repeat ; Male ; Minority & ethnic groups ; Native Americans ; Nucleotides ; Peru ; Plasmids ; Polymerase chain reaction ; Polymorphism, Single Nucleotide ; Recombination ; Sequence Deletion ; Single-nucleotide polymorphism ; Terminal Repeat Sequences ; Transfection</subject><ispartof>Transfusion (Philadelphia, Pa.), 2019-07, Vol.59 (7), p.2415-2421</ispartof><rights>2019 AABB</rights><rights>2019 AABB.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4198-c994c8eb884e8d194deebddd75d59e8ff864a3142068df29cb3c9d8dbc48fe023</citedby><cites>FETCH-LOGICAL-c4198-c994c8eb884e8d194deebddd75d59e8ff864a3142068df29cb3c9d8dbc48fe023</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,778,782,27911,27912</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30957248$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Soejima, Mikiko</creatorcontrib><creatorcontrib>Koda, Yoshiro</creatorcontrib><title>Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR‐mediated deletion and characterization of 4 nonsynonymous single‐nucleotide polymorphisms</title><title>Transfusion (Philadelphia, Pa.)</title><addtitle>Transfusion</addtitle><description>BACKGROUND
The human FUT2 gene, which encodes a secretor type α(1,2)fucosyltransferase, is reported to have several population‐specific single‐nucleotide polymorphisms (SNPs) and copy number variations. However, little is known about genetic variation of FUT2 in Native Americans.
STUDY DESIGN AND METHODS
To detect SNPs and copy number variations of the FUT2 gene in Peruvians, direct sequencing and digital polymerase chain reaction were performed. Haplotypes of observed SNPs were estimated by PHASE software or cloning into plasmids. The functional significance of nonsynonymous SNPs was examined by transient transfection assay.
RESULTS
We identified three novel nonfunctional alleles (se178,357, se841, and sedel4) due to two nonsynonymous SNPs (178C > T and 841G > A) and a novel long terminal repeat–mediated recombination with a 4.3‐kb deletion in 70 Peruvians. The frequency of nonfunctional alleles was relative low (20.7%). Because se841 has a relatively high frequency (5.7%), it might be a suitable genetic marker for Peruvians.
CONCLUSION
We identified three novel nonfunctional alleles in 70 Peruvians. To our knowledge, this is the first time a long terminal repeat–mediated gene recombination event at the FUT2 locus has been detected.</description><subject>Alleles</subject><subject>Base Sequence</subject><subject>Clonal deletion</subject><subject>Cloning</subject><subject>Copy number</subject><subject>DNA Copy Number Variations</subject><subject>Female</subject><subject>Fucosyltransferases - genetics</subject><subject>FUT2 gene</subject><subject>Galactoside 2-alpha-L-fucosyltransferase</subject><subject>Gene deletion</subject><subject>Gene Frequency</subject><subject>Gene sequencing</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Haplotypes</subject><subject>Humans</subject><subject>Indians, South American - genetics</subject><subject>Long terminal repeat</subject><subject>Male</subject><subject>Minority & ethnic groups</subject><subject>Native Americans</subject><subject>Nucleotides</subject><subject>Peru</subject><subject>Plasmids</subject><subject>Polymerase chain reaction</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Recombination</subject><subject>Sequence Deletion</subject><subject>Single-nucleotide polymorphism</subject><subject>Terminal Repeat Sequences</subject><subject>Transfection</subject><issn>0041-1132</issn><issn>1537-2995</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><recordid>eNp1kUFOGzEUhi1URALtoheoLHXVxRDb4yF2dxVqKFIkEErWI4_9XBxN7Kk9ExRWHKE36Z04SU0C2eGFvfD3vl96P0KfKTmn-Uz6aM9pxaQ4QmNaldOCSVl9QGNCOC0oLdkInaa0IoQwSegJGpVEVlPGxRj9uwIPvdN4o6JTvQseB4tnywXDzmOFbyEOG6c87kI3tDvgO3YGfO-s04cBhX3YQIvni7vnp79rMNkFBhtoYYcob7C-V1HpHqJ7PMzxPOfTNl_bdRgSTs7_biEr_KBbCH1Oyslt_ozdvUvr9BEdW9Um-PT6nqHl7Ofi8lcxv7m6vvwxLzSnUhRaSq4FNEJwEIZKbgAaY8y0MpUEYa244KqknJELYSyTuim1NMI0mgsLhJVn6Ove28XwZ4DU16swRJ8ja8YqSgln7IX6tqd0DClFsHUX3VrFbU1J_VJNnaupd9Vk9surcWjygg7kWxcZmOyBB9fC9n1Tvbib7ZX_ASEZnxg</recordid><startdate>201907</startdate><enddate>201907</enddate><creator>Soejima, Mikiko</creator><creator>Koda, Yoshiro</creator><general>John Wiley & Sons, Inc</general><general>Wiley Subscription Services, Inc</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>7QO</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope></search><sort><creationdate>201907</creationdate><title>Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR‐mediated deletion and characterization of 4 nonsynonymous single‐nucleotide polymorphisms</title><author>Soejima, Mikiko ; Koda, Yoshiro</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4198-c994c8eb884e8d194deebddd75d59e8ff864a3142068df29cb3c9d8dbc48fe023</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Alleles</topic><topic>Base Sequence</topic><topic>Clonal deletion</topic><topic>Cloning</topic><topic>Copy number</topic><topic>DNA Copy Number Variations</topic><topic>Female</topic><topic>Fucosyltransferases - genetics</topic><topic>FUT2 gene</topic><topic>Galactoside 2-alpha-L-fucosyltransferase</topic><topic>Gene deletion</topic><topic>Gene Frequency</topic><topic>Gene sequencing</topic><topic>Genetic diversity</topic><topic>Genetic markers</topic><topic>Haplotypes</topic><topic>Humans</topic><topic>Indians, South American - genetics</topic><topic>Long terminal repeat</topic><topic>Male</topic><topic>Minority & ethnic groups</topic><topic>Native Americans</topic><topic>Nucleotides</topic><topic>Peru</topic><topic>Plasmids</topic><topic>Polymerase chain reaction</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Recombination</topic><topic>Sequence Deletion</topic><topic>Single-nucleotide polymorphism</topic><topic>Terminal Repeat Sequences</topic><topic>Transfection</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Soejima, Mikiko</creatorcontrib><creatorcontrib>Koda, Yoshiro</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><jtitle>Transfusion (Philadelphia, Pa.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Soejima, Mikiko</au><au>Koda, Yoshiro</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR‐mediated deletion and characterization of 4 nonsynonymous single‐nucleotide polymorphisms</atitle><jtitle>Transfusion (Philadelphia, Pa.)</jtitle><addtitle>Transfusion</addtitle><date>2019-07</date><risdate>2019</risdate><volume>59</volume><issue>7</issue><spage>2415</spage><epage>2421</epage><pages>2415-2421</pages><issn>0041-1132</issn><eissn>1537-2995</eissn><abstract>BACKGROUND
The human FUT2 gene, which encodes a secretor type α(1,2)fucosyltransferase, is reported to have several population‐specific single‐nucleotide polymorphisms (SNPs) and copy number variations. However, little is known about genetic variation of FUT2 in Native Americans.
STUDY DESIGN AND METHODS
To detect SNPs and copy number variations of the FUT2 gene in Peruvians, direct sequencing and digital polymerase chain reaction were performed. Haplotypes of observed SNPs were estimated by PHASE software or cloning into plasmids. The functional significance of nonsynonymous SNPs was examined by transient transfection assay.
RESULTS
We identified three novel nonfunctional alleles (se178,357, se841, and sedel4) due to two nonsynonymous SNPs (178C > T and 841G > A) and a novel long terminal repeat–mediated recombination with a 4.3‐kb deletion in 70 Peruvians. The frequency of nonfunctional alleles was relative low (20.7%). Because se841 has a relatively high frequency (5.7%), it might be a suitable genetic marker for Peruvians.
CONCLUSION
We identified three novel nonfunctional alleles in 70 Peruvians. To our knowledge, this is the first time a long terminal repeat–mediated gene recombination event at the FUT2 locus has been detected.</abstract><cop>Hoboken, USA</cop><pub>John Wiley & Sons, Inc</pub><pmid>30957248</pmid><doi>10.1111/trf.15298</doi><tpages>7</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0041-1132 |
| ispartof | Transfusion (Philadelphia, Pa.), 2019-07, Vol.59 (7), p.2415-2421 |
| issn | 0041-1132 1537-2995 |
| language | eng |
| recordid | cdi_proquest_journals_2251104222 |
| source | Wiley-Blackwell Read & Publish Collection |
| subjects | Alleles Base Sequence Clonal deletion Cloning Copy number DNA Copy Number Variations Female Fucosyltransferases - genetics FUT2 gene Galactoside 2-alpha-L-fucosyltransferase Gene deletion Gene Frequency Gene sequencing Genetic diversity Genetic markers Haplotypes Humans Indians, South American - genetics Long terminal repeat Male Minority & ethnic groups Native Americans Nucleotides Peru Plasmids Polymerase chain reaction Polymorphism, Single Nucleotide Recombination Sequence Deletion Single-nucleotide polymorphism Terminal Repeat Sequences Transfection |
| title | Genetic variation of FUT2 in a Peruvian population: identification of a novel LTR‐mediated deletion and characterization of 4 nonsynonymous single‐nucleotide polymorphisms |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-15T16%3A54%3A41IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genetic%20variation%20of%20FUT2%20in%20a%20Peruvian%20population:%20identification%20of%20a%20novel%20LTR%E2%80%90mediated%20deletion%20and%20characterization%20of%204%20nonsynonymous%20single%E2%80%90nucleotide%20polymorphisms&rft.jtitle=Transfusion%20(Philadelphia,%20Pa.)&rft.au=Soejima,%20Mikiko&rft.date=2019-07&rft.volume=59&rft.issue=7&rft.spage=2415&rft.epage=2421&rft.pages=2415-2421&rft.issn=0041-1132&rft.eissn=1537-2995&rft_id=info:doi/10.1111/trf.15298&rft_dat=%3Cproquest_cross%3E2251104222%3C/proquest_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c4198-c994c8eb884e8d194deebddd75d59e8ff864a3142068df29cb3c9d8dbc48fe023%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2251104222&rft_id=info:pmid/30957248&rfr_iscdi=true |