Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia

Among other applications of long-distance haplotype phasing in clinical genetics, determination of linked DNA markers as surrogate for problematic structural variants (e.g., repeat-mediated rearrangements) is essential to perform diagnosis from low-quality DNA samples. We describe a next-of-kin-inde...

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Autores: Abelleyro, Miguel Martin, Marchione, Vanina Daniela, Palmitelli, Micaela, Radic, Claudia Pamela, Neme, Daniela, Larripa, Irene Beatriz, Medina Acosta, Enrique, de Brasi, Carlos Daniel, Rossetti, Liliana Carmen
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:Argentina
Institución:Consejo Nacional de Investigaciones Científicas y Técnicas
Repositorio:CONICET Digital (CONICET)
Idioma:inglés
OAI Identifier:oai:ri.conicet.gov.ar:11336/103574
Acceso en línea:http://hdl.handle.net/11336/103574
Access Level:acceso abierto
Palabra clave:F8
HEMA
STR
INV22
https://purl.org/becyt/ford/3.1
https://purl.org/becyt/ford/3
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oai_identifier_str oai:ri.conicet.gov.ar:11336/103574
network_acronym_str AR
network_name_str Argentina
repository_id_str
dc.title.none.fl_str_mv Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia
title Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia
spellingShingle Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia
Abelleyro, Miguel Martin
F8
HEMA
STR
INV22
https://purl.org/becyt/ford/3.1
https://purl.org/becyt/ford/3
title_short Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia
title_full Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia
title_fullStr Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia
title_full_unstemmed Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia
title_sort Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia
dc.creator.none.fl_str_mv Abelleyro, Miguel Martin
Marchione, Vanina Daniela
Palmitelli, Micaela
Radic, Claudia Pamela
Neme, Daniela
Larripa, Irene Beatriz
Medina Acosta, Enrique
de Brasi, Carlos Daniel
Rossetti, Liliana Carmen
author Abelleyro, Miguel Martin
author_facet Abelleyro, Miguel Martin
Marchione, Vanina Daniela
Palmitelli, Micaela
Radic, Claudia Pamela
Neme, Daniela
Larripa, Irene Beatriz
Medina Acosta, Enrique
de Brasi, Carlos Daniel
Rossetti, Liliana Carmen
author_role author
author2 Marchione, Vanina Daniela
Palmitelli, Micaela
Radic, Claudia Pamela
Neme, Daniela
Larripa, Irene Beatriz
Medina Acosta, Enrique
de Brasi, Carlos Daniel
Rossetti, Liliana Carmen
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv F8
HEMA
STR
INV22
https://purl.org/becyt/ford/3.1
https://purl.org/becyt/ford/3
topic F8
HEMA
STR
INV22
https://purl.org/becyt/ford/3.1
https://purl.org/becyt/ford/3
description Among other applications of long-distance haplotype phasing in clinical genetics, determination of linked DNA markers as surrogate for problematic structural variants (e.g., repeat-mediated rearrangements) is essential to perform diagnosis from low-quality DNA samples. We describe a next-of-kin-independent (physical) phasing approach based on inverse-PCR (iPCR) paired-end amplification (PI). This method enables typing the multialleles of the short tandem repeat (STR) F8Int21[CA]n at the F8-intron 21, as a surrogate DNA marker for the F8-intron 22 inversion (Inv22), the hemophilia A-causative hotspot, within the transmitted haplotype in informative carriers. We provide proof-of-concept by blindly validating the PI approach in 15 carrier mother/affected-son duos. Every F8Int21[CA]n STR allele determined in phase with the Inv22 allele in the female carriers from the informative duos was confirmed in the hemizygous proband (P = 0.00003). A second surrogate STR locus at the F8-IVS22 was obtained by the PI approach improving severe-HA preimplantation genetic diagnosis by augmenting heterozygosity in Inv22 carriers bypassing the requirement for family linkage analysis. The ability of the PI-assay to combine other marker pairs was demonstrated by haplotyping a SNV (F8:c.6118T > C) with a >28kb-distant F8-IVS22 STR. The PI approach has proven flexibility to target different marker pairs and has potential for multiplex characterization of iPCR products by massively parallel sequencing.
publishDate 2019
dc.date.none.fl_str_mv 2019-01
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/103574
Abelleyro, Miguel Martin; Marchione, Vanina Daniela; Palmitelli, Micaela; Radic, Claudia Pamela; Neme, Daniela; et al.; Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia; Nature Publishing Group; European Journal Of Human Genetics; 27; 4; 1-2019; 603-611
1018-4813
CONICET Digital
CONICET
url http://hdl.handle.net/11336/103574
identifier_str_mv Abelleyro, Miguel Martin; Marchione, Vanina Daniela; Palmitelli, Micaela; Radic, Claudia Pamela; Neme, Daniela; et al.; Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia; Nature Publishing Group; European Journal Of Human Genetics; 27; 4; 1-2019; 603-611
1018-4813
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1038/s41431-018-0334-9
info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41431-018-0334-9
info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460640/
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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spelling Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophiliaAbelleyro, Miguel MartinMarchione, Vanina DanielaPalmitelli, MicaelaRadic, Claudia PamelaNeme, DanielaLarripa, Irene BeatrizMedina Acosta, Enriquede Brasi, Carlos DanielRossetti, Liliana CarmenF8HEMASTRINV22https://purl.org/becyt/ford/3.1https://purl.org/becyt/ford/3Among other applications of long-distance haplotype phasing in clinical genetics, determination of linked DNA markers as surrogate for problematic structural variants (e.g., repeat-mediated rearrangements) is essential to perform diagnosis from low-quality DNA samples. We describe a next-of-kin-independent (physical) phasing approach based on inverse-PCR (iPCR) paired-end amplification (PI). This method enables typing the multialleles of the short tandem repeat (STR) F8Int21[CA]n at the F8-intron 21, as a surrogate DNA marker for the F8-intron 22 inversion (Inv22), the hemophilia A-causative hotspot, within the transmitted haplotype in informative carriers. We provide proof-of-concept by blindly validating the PI approach in 15 carrier mother/affected-son duos. Every F8Int21[CA]n STR allele determined in phase with the Inv22 allele in the female carriers from the informative duos was confirmed in the hemizygous proband (P = 0.00003). A second surrogate STR locus at the F8-IVS22 was obtained by the PI approach improving severe-HA preimplantation genetic diagnosis by augmenting heterozygosity in Inv22 carriers bypassing the requirement for family linkage analysis. The ability of the PI-assay to combine other marker pairs was demonstrated by haplotyping a SNV (F8:c.6118T > C) with a >28kb-distant F8-IVS22 STR. The PI approach has proven flexibility to target different marker pairs and has potential for multiplex characterization of iPCR products by massively parallel sequencing.Fil: Abelleyro, Miguel Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; ArgentinaFil: Marchione, Vanina Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; ArgentinaFil: Palmitelli, Micaela. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; ArgentinaFil: Radic, Claudia Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; ArgentinaFil: Neme, Daniela. Fundación de la Hemofilia Alfredo Pavlovsky; ArgentinaFil: Larripa, Irene Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; ArgentinaFil: Medina Acosta, Enrique. Universidade Estadual Do Norte Fluminense Darcy Ribeiro; BrasilFil: de Brasi, Carlos Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; Argentina. Academia Nacional de Medicina de Buenos Aires. Instituto de Investigaciones Hematológicas "Mariano R. Castex"; ArgentinaFil: Rossetti, Liliana Carmen. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; ArgentinaNature Publishing Group2019-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/103574Abelleyro, Miguel Martin; Marchione, Vanina Daniela; Palmitelli, Micaela; Radic, Claudia Pamela; Neme, Daniela; et al.; Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia; Nature Publishing Group; European Journal Of Human Genetics; 27; 4; 1-2019; 603-6111018-4813CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1038/s41431-018-0334-9info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41431-018-0334-9info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460640/info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2024-05-08T14:18:13Zoai:ri.conicet.gov.ar:11336/103574instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982024-05-08 14:18:13.535CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
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