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Abelleyro MM, Marchione VD, Palmitelli M, Radic CP, Neme D, Larripa IB, Medina-Acosta E, De Brasi CD, Rossetti LC. Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia. Eur J Hum Genet 2019; 27:603-611. [PMID: 30626931 DOI: 10.1038/s41431-018-0334-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 12/30/2022] Open
Abstract
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.
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Affiliation(s)
- Miguel Martín Abelleyro
- Instituto de Medicina Experimental (IMEX), CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Vanina Daniela Marchione
- Instituto de Medicina Experimental (IMEX), CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Micaela Palmitelli
- Instituto de Medicina Experimental (IMEX), CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Claudia Pamela Radic
- Instituto de Medicina Experimental (IMEX), CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Daniela Neme
- Fundación de la Hemofilia Alfredo Pavlovsky, Buenos Aires, Argentina
| | - Irene Beatriz Larripa
- Instituto de Medicina Experimental (IMEX), CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Enrique Medina-Acosta
- Universidade Estadual do Norte Fluminense Darcy Ribeiro, Centro de Biociências e Biotecnologia, Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Carlos Daniel De Brasi
- Instituto de Medicina Experimental (IMEX), CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina.,Instituto de Investigaciones Hematológicas Mariano R Castex, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Liliana Carmen Rossetti
- Instituto de Medicina Experimental (IMEX), CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina.
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Cao Y, Shen L, Huang R, Yang L, Du Z, Ma H, Zheng T, Gu H, Li H. Direct and indirect gene diagnosis of hemophilia A pedigrees in the Chinese population. Mol Med Rep 2017; 16:5722-5728. [PMID: 28849064 DOI: 10.3892/mmr.2017.7263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 06/16/2017] [Indexed: 11/06/2022] Open
Abstract
Hemophilia A (HA) is an X‑linked recessive hereditary disorder caused by defects in the coagulation factor VIII (FVIII) gene. In order to diagnose patients with presymptomatic HA and carriers, the present study conducted direct gene diagnosis for the common abnormalities in FVIII and subsequently performed indirect gene diagnosis for the other abnormalities in FVIII for Chinese HA pedigrees. Direct gene diagnosis was performed in 10 HA pedigrees using inverse shifting‑polymerase chain reaction to detect intron 22 inversion (inv22), intron 22 deletion, intron 22 duplication and inv1 of FVIII. Pedigrees with no detected mutations were further analyzed using indirect genetic diagnosis (haplotype linkage analysis), where the genetic markers of FVIII included one variable number of tandem repeat, seven short tandem repeats and three restriction fragment length polymorphisms. The results of three pedigrees were taken as examples. Pedigree 1 underwent direct gene diagnosis, which demonstrated that the proband was inv22 distal pattern hemophiliac and the mother was an inv22 distal pattern carrier. The other two pedigrees were subjected to indirect gene diagnosis. In pedigree 2, the detection of DXS52, 13(CA) n, DXS9901(GT) n, intron (int)18, int19 and int22 confirmed the proband's baby brother was normal, the proband's maternal aunt was a carrier and her baby son was normal. Detection of DXS9901(GT)n, int18, int19 and int22 in pedigree 3 demonstrated that the proband's maternal grandmother was not a carrier. As the maternal grandfather was not affected by the disease, it was deduced that a mutation of FVIII occurred in the proband's mother. The combination of direct and indirect gene diagnoses provides reliable evidence for the use of genetic counseling in HA pedigrees, particularly for screening presymptomatic males and female carriers with normal offspring.
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Affiliation(s)
- Ying Cao
- The Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Luxi Shen
- Department of Graduate Students, Xuanwu Hospital, Capital Medical University, Beijing 100053, P.R. China
| | - Rong Huang
- The Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Lingcong Yang
- The Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Zhuanyun Du
- The Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Hua Ma
- The Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Tianjin Zheng
- Department of Technical Guidance, Family Planning Publicity and Technical Guidance Station of Wenzhou City, Wenzhou, Zhejiang 325000, P.R. China
| | - Haihua Gu
- The Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
| | - Hongzhi Li
- The Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China
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Shrestha S, Dong S, Li Z, Huang Z, Zheng F. Evaluation of factor VIII polymorphic short tandem repeat markers in linkage analysis for carrier diagnosis of hemophilia A. Biomed Rep 2016; 5:228-232. [PMID: 27446547 DOI: 10.3892/br.2016.712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/10/2016] [Indexed: 11/06/2022] Open
Abstract
Hemophilia A (HA) is the most common inherited X-linked recessive bleeding disorder caused by heterogeneous mutations in the factor VIII gene (FVIII). Diagnosis of the carrier is critical for preventing the birth of children affected by this coagulation disorder, which ultimately facilitates its management. Due to the heterogeneous nature of mutations, the large inversions and the complexity of the FVIII gene, direct recognition of the disease-associated mutation in HA is complex. Indirect linkage analysis using highly informative heterozygous polymorphic markers is an alternative method for determining the co-segregation of the mutant gene within a family for carrier detection of HA. The aim of the present study was to perform carrier diagnosis in a family with HA. Rapid multifluorescent polymerase chain reaction (PCR) was performed with six extragenic short tandem repeats (STRs), DXS1073, DXS15, DXS8091, DXS1227, DXS991, DXS993 and one intragenic marker, STR22 for linkage analysis in the HA family. All the STR markers employed in the present study were informative for linkages of pathogenic and healthy haplotypes among family members, particularly STR22, DXS1073 and DXS15. The STR marker, STR22, is within the FVIII gene while the DXS1073 and DXS15 markers are very close to the FVIII gene, where the chances of recombination are comparatively low, and provided the most accurate interpretation analysis, indicating that the proband's sister may have been the HA carrier. Rapid multifluorescent PCR using STR markers and linkage analysis was identified to be a simple method for performing HA carrier diagnosis.
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Affiliation(s)
- Sabina Shrestha
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Sufang Dong
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Zuhua Li
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Zhuliang Huang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Fang Zheng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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Garagiola I, Seregni S, Mortarino M, Mancuso ME, Fasulo MR, Notarangelo LD, Peyvandi F. A recurrent F8 mutation (c.6046C>T) causing hemophilia A in 8% of northern Italian patients: evidence for a founder effect. Mol Genet Genomic Med 2015; 4:152-9. [PMID: 27066508 PMCID: PMC4799873 DOI: 10.1002/mgg3.189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 10/23/2015] [Accepted: 10/27/2015] [Indexed: 11/10/2022] Open
Abstract
Hemophilia A is a heterogeneous hemorrhagic disorder caused by a large number of mutations. Recurrent mutations are rare, except intron 22 and intron 1 inversions. The substitution of a cytosine to a thymine at nucleotide 6046 in F8 gene was identified in a group of Italian patients affected by hemophilia A from a specific region of Northern Italy with a prevalence of 7.6%. This F8 variant was the second most frequent mutation in our cohort, after the intron 22 inversion. The identification of the same mutation in a restricted population gets to suppose the existence of a founder effect. Intragenic and extragenic polymorphic markers were tested to assess this assumption. A peculiar haplotype in linkage disequilibrium with this recurrent mutation (c.6046C>T) was identified in 71% of patients, supporting a founder effect. This distinctive haplotype was not identified in a control group (Fisher's exact test, P < 0.0001), coming from the same geographic region. These data strongly suggested the presence of a founder effect, supporting the existence of a single mutation event. Using DMLE+2.3 software and the mathematical approach described by Bengtsson and Thomson, the inferred age of this mutation is supposed to be about 2325 years (95% CI: 904–5081) ago.
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Affiliation(s)
- Isabella Garagiola
- Angelo Bianchi Bonomi Haemophilia and Thrombosis Center Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Università degli Studi di Milano and Luigi Villa Foundation Milan Italy
| | - Sabrina Seregni
- Angelo Bianchi Bonomi Haemophilia and Thrombosis Center Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Università degli Studi di Milano and Luigi Villa Foundation Milan Italy
| | - Mimosa Mortarino
- Angelo Bianchi Bonomi Haemophilia and Thrombosis Center Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Università degli Studi di Milano and Luigi Villa Foundation Milan Italy
| | - Maria Elisa Mancuso
- Angelo Bianchi Bonomi Haemophilia and Thrombosis Center Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Università degli Studi di Milano and Luigi Villa Foundation Milan Italy
| | - Maria Rosaria Fasulo
- Angelo Bianchi Bonomi Haemophilia and Thrombosis Center Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Università degli Studi di Milano and Luigi Villa Foundation Milan Italy
| | | | - Flora Peyvandi
- Angelo Bianchi Bonomi Haemophilia and Thrombosis Center Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Università degli Studi di Milano and Luigi Villa Foundation Milan Italy
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Abelleyro MM, Rossetti LC, Curto MDLÁ, Radic CP, Marchione VD, De Brasi CD. F8 intron 22 inversions and SNP rs73563631 in unrelated families with severe haemophilia A: clinical features and gene testing implications. Thromb Haemost 2015; 115:678-81. [PMID: 26489971 DOI: 10.1160/th15-08-0643] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/13/2015] [Indexed: 11/05/2022]
Abstract
Supplementary Material to this article is available online at www.thrombosis-online.com.
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Affiliation(s)
| | | | | | | | | | - Carlos Daniel De Brasi
- Carlos D. De Brasi, Molecular Genetics of Haemophilia Laboratory, Academia Nacional de Medicina, Pacheco de Melo 3081, Buenos Aires (1425), Argentina, Tel.: +5411 48058803, Ext.: 261, Fax: +5411 4803 9475, E-mail:
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Massaro JD, Wiezel CEV, Muniz YCN, Rego EM, de Oliveira LCO, Mendes-Junior CT, Simões AL. Analysis of five polymorphic DNA markers for indirect genetic diagnosis of haemophilia A in the Brazilian population. Haemophilia 2011; 17:e936-43. [PMID: 21649803 DOI: 10.1111/j.1365-2516.2011.02592.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hemophilia A is an X-linked, inherited, bleeding disorder caused by the partial or total inactivity of the coagulation factor VIII (FVIII). Due to difficulties in the direct recognition of the disease-associated mutation in the F8 gene, indirect diagnosis using polymorphic markers located inside or close to the gene is used as an alternative for determining the segregation of the mutant gene within families and thus for detecting carrier individuals and/or assisting in prenatal diagnosis. This study characterizes the allelic and haplotype frequencies, genetic diversity, population differentiation and linkage disequilibrium of five microsatellites (F8Int1, F8Int13, F8Int22, F8Int25.3 and IKBKG) in samples of healthy individuals from São Paulo, Rio Grande do Sul and Pernambuco and of patients from São Paulo with haemophilia A to determine the degree of informativeness of these microsatellites for diagnostic purposes. The interpopulational diversity parameters highlight the differences among the analyzed population samples. Regional differences in allelic frequencies must be taken into account when conducting indirect diagnosis of haemophilia A. With the exception of IKBKG, all of the microsatellites presented high heterozygosity levels. Using the markers described, diagnosis was possible in 10 of 11 families. The F8Int22, F8Int1, F8Int13, F8Int25.3 and IKBKG microsatellites were informative in seven, six, five and two of the cases, respectively, demonstrating the effectiveness of using these microsatellites in prenatal diagnosis and in carrier identification in the Brazilian population.
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Affiliation(s)
- J D Massaro
- Departments of GeneticsMedical Clinic, School of Medicine of Ribeirão Preto, University of São Paulo, Brazil
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Current world literature. Curr Opin Obstet Gynecol 2010; 22:166-75. [PMID: 20216348 DOI: 10.1097/gco.0b013e328338c956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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