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Copy number variations in endoglin locus: mapping of large deletions in Spanish families with hereditary hemorrhagic telangiectasia type 1.

Fontalba A, Fernández-Luna JL, Zarrabeitia R, Recio-Poveda L, Albiñana V, Ojeda-Fernández ML, Bernabéu C, Alcaraz LA, Botella LM - BMC Med. Genet. (2013)

Bottom Line: The array was designed to cover the ENG gene and surrounding areas.Interestingly, common breakpoints coincident with Alu repetitive sequences were found among these families.The systematic hybridization of DNA from HHT families, with deletions or duplications, to custom designed microarrays, could allow the mapping of breakpoints, coincident with repetitive Alu sequences that might act as "hot spots" in the development of chromosomal anomalies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. cibluisa@cib.csic.es.

ABSTRACT

Background: The hereditary hemorrhagic telangiectasia syndrome (HHT), also known as the Rendu-Osler-Weber syndrome is a multiorganic vascular disorder inherited as an autosomal dominant trait. Diagnostic clinical criteria include: epistaxis, telangiectases in mucocutaneous and gastrointestinal sites, arteriovenous malformations (AVMs) most commonly found in pulmonary, hepatic and cerebral circulations, and familial inheritance. HHT is transmitted in 90% of the cases as an autosomal dominant condition due to mutations in either endoglin (ENG), or activin receptor-like kinase 1 (ACVRL1/ALK1) genes (HHT type 1 and 2, respectively).

Methods: We have carried out a genetic analysis of four independent Spanish families with HHT clinical criteria, which has permitted the identification of new large deletions in ENG. These mutations were first detected using the MLPA technique and subsequently, the deletion breakpoints were mapped using a customized copy number variation (CNV) microarray. The array was designed to cover the ENG gene and surrounding areas.

Results: All tested families carried large deletions ranging from 3-kb to 100-kb, involving the ENG gene promoter, several ENG exons, and the two downstream genes FGSH and CDK9. Interestingly, common breakpoints coincident with Alu repetitive sequences were found among these families.

Conclusions: The systematic hybridization of DNA from HHT families, with deletions or duplications, to custom designed microarrays, could allow the mapping of breakpoints, coincident with repetitive Alu sequences that might act as "hot spots" in the development of chromosomal anomalies.

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Related in: MedlinePlus

Schematic representation of the probes covering the ENG gene and its flanking regions on the human chromosome 9. The probes overlap centered at ENG (tiling microarray).
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Figure 1: Schematic representation of the probes covering the ENG gene and its flanking regions on the human chromosome 9. The probes overlap centered at ENG (tiling microarray).

Mentions: Breakpoints were studied using a custom designed CGH microarray (Agilent) to detect copy number variations. A tiling microarray was designed with eArray (Agilent). The array contains a total of 15,744 probes, including: i) 7,568 probes of ENG; ii) 3,927 probes from the rest of chromosome 9; iii) 1,262 probes included for normalization; and iv) 2,987 probes as Agilent controls. A total of 7,568 probes were selected in the region of interest (chr9: 130548305–130661871, hg19) covering the ENG gene and the surrounding upstream and downstream sequences to complete a total area of 113-Kb, with the ENG gene in its center (Figure 1). Probes were designed with an average probe spacing of 15-bp, and allowed to vary in size (from 45- to 60-mer) in order to maintain their Tm about 80°C. The rest of the chromosome 9 was covered with 3,927 additional probes. For normalization purposes during data analysis, 1,262 probes, distributed among all chromosomes, were also included. 2,987 probes were Agilent controls. A probe performance score was assigned to each probe by the software.


Copy number variations in endoglin locus: mapping of large deletions in Spanish families with hereditary hemorrhagic telangiectasia type 1.

Fontalba A, Fernández-Luna JL, Zarrabeitia R, Recio-Poveda L, Albiñana V, Ojeda-Fernández ML, Bernabéu C, Alcaraz LA, Botella LM - BMC Med. Genet. (2013)

Schematic representation of the probes covering the ENG gene and its flanking regions on the human chromosome 9. The probes overlap centered at ENG (tiling microarray).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222255&req=5

Figure 1: Schematic representation of the probes covering the ENG gene and its flanking regions on the human chromosome 9. The probes overlap centered at ENG (tiling microarray).
Mentions: Breakpoints were studied using a custom designed CGH microarray (Agilent) to detect copy number variations. A tiling microarray was designed with eArray (Agilent). The array contains a total of 15,744 probes, including: i) 7,568 probes of ENG; ii) 3,927 probes from the rest of chromosome 9; iii) 1,262 probes included for normalization; and iv) 2,987 probes as Agilent controls. A total of 7,568 probes were selected in the region of interest (chr9: 130548305–130661871, hg19) covering the ENG gene and the surrounding upstream and downstream sequences to complete a total area of 113-Kb, with the ENG gene in its center (Figure 1). Probes were designed with an average probe spacing of 15-bp, and allowed to vary in size (from 45- to 60-mer) in order to maintain their Tm about 80°C. The rest of the chromosome 9 was covered with 3,927 additional probes. For normalization purposes during data analysis, 1,262 probes, distributed among all chromosomes, were also included. 2,987 probes were Agilent controls. A probe performance score was assigned to each probe by the software.

Bottom Line: The array was designed to cover the ENG gene and surrounding areas.Interestingly, common breakpoints coincident with Alu repetitive sequences were found among these families.The systematic hybridization of DNA from HHT families, with deletions or duplications, to custom designed microarrays, could allow the mapping of breakpoints, coincident with repetitive Alu sequences that might act as "hot spots" in the development of chromosomal anomalies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. cibluisa@cib.csic.es.

ABSTRACT

Background: The hereditary hemorrhagic telangiectasia syndrome (HHT), also known as the Rendu-Osler-Weber syndrome is a multiorganic vascular disorder inherited as an autosomal dominant trait. Diagnostic clinical criteria include: epistaxis, telangiectases in mucocutaneous and gastrointestinal sites, arteriovenous malformations (AVMs) most commonly found in pulmonary, hepatic and cerebral circulations, and familial inheritance. HHT is transmitted in 90% of the cases as an autosomal dominant condition due to mutations in either endoglin (ENG), or activin receptor-like kinase 1 (ACVRL1/ALK1) genes (HHT type 1 and 2, respectively).

Methods: We have carried out a genetic analysis of four independent Spanish families with HHT clinical criteria, which has permitted the identification of new large deletions in ENG. These mutations were first detected using the MLPA technique and subsequently, the deletion breakpoints were mapped using a customized copy number variation (CNV) microarray. The array was designed to cover the ENG gene and surrounding areas.

Results: All tested families carried large deletions ranging from 3-kb to 100-kb, involving the ENG gene promoter, several ENG exons, and the two downstream genes FGSH and CDK9. Interestingly, common breakpoints coincident with Alu repetitive sequences were found among these families.

Conclusions: The systematic hybridization of DNA from HHT families, with deletions or duplications, to custom designed microarrays, could allow the mapping of breakpoints, coincident with repetitive Alu sequences that might act as "hot spots" in the development of chromosomal anomalies.

Show MeSH
Related in: MedlinePlus