Incidence of amplification failure in DMPK allele due to allelic dropout event in a diagnostic laboratory

Claudia De Siena, Rosanna Cardani, Elisa Brigonzi, Francesca Bosè, Barbara Fossati, Giovanni Meola, Elena Costa, Rea Valaperta

Research output: Contribution to journalArticle

Abstract

Background: Myotonic dystrophy type 1 (DM1) is caused by an expanded CTG repeat in the non-coding 3’ UTR of the DMPK gene. PCR and Southern Blot Analysis (SBA) of long-range PCR represent the routine molecular testing most widely used for DM1 diagnosis. However, in these conventional methods artifacts such as allele dropout (ADO) represent a risk of misdiagnosis for DM1. Subjects, who show a single product by conventional methods, require a complementary technique such as triplet repeat primed PCR (TP-PCR). Object: To estimate and minimize the incidence of allele dropout event in our diagnostic molecular laboratory by the use of new kit TP-PCR-based. Methods: We retrospectively studied 190 DMPK alleles, on blood samples from to ninety-five subjects, previously genotyped by traditional methods to validate a new assay. The pedigree of a DM1 family was used to expand our analysis. Results: TP-PCR assay correctly identified all 95/95 (100%) subjects and these results were in agreement with the other molecular laboratory. By conventional methods the amplification failure due to allele dropout in our cohort was in 12/190 (6.3%) DMPK alleles analyzed. When these 12 alleles were detected and solved by new assay, we found that the 2.6% was caused by primer sequence-dependent and the remaining 3.6% by polymerase-hindering secondary structures. Conclusions: Allele dropout could be considered as a potentially important problem in DM1 diagnosis that may lead to the attribution of a wrong genotype with long-term consequences for both proband and family.

Original languageEnglish
Pages (from-to)111-116
Number of pages6
JournalClinica Chimica Acta
Volume484
DOIs
Publication statusPublished - Sep 1 2018

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Trinucleotide Repeats
Amplification
Assays
Alleles
Incidence
Polymerase Chain Reaction
3' Untranslated Regions
Blood
Genes
Testing
Myotonic Dystrophy
Molecular Pathology
Pedigree
Southern Blotting
Diagnostic Errors
Artifacts
Genotype

Keywords

  • Diagnostic error
  • Interruptions
  • Myotonic dystrophy type 1
  • TP-PCR technique

ASJC Scopus subject areas

  • Biochemistry
  • Clinical Biochemistry
  • Biochemistry, medical

Cite this

Incidence of amplification failure in DMPK allele due to allelic dropout event in a diagnostic laboratory. / De Siena, Claudia; Cardani, Rosanna; Brigonzi, Elisa; Bosè, Francesca; Fossati, Barbara; Meola, Giovanni; Costa, Elena; Valaperta, Rea.

In: Clinica Chimica Acta, Vol. 484, 01.09.2018, p. 111-116.

Research output: Contribution to journalArticle

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abstract = "Background: Myotonic dystrophy type 1 (DM1) is caused by an expanded CTG repeat in the non-coding 3’ UTR of the DMPK gene. PCR and Southern Blot Analysis (SBA) of long-range PCR represent the routine molecular testing most widely used for DM1 diagnosis. However, in these conventional methods artifacts such as allele dropout (ADO) represent a risk of misdiagnosis for DM1. Subjects, who show a single product by conventional methods, require a complementary technique such as triplet repeat primed PCR (TP-PCR). Object: To estimate and minimize the incidence of allele dropout event in our diagnostic molecular laboratory by the use of new kit TP-PCR-based. Methods: We retrospectively studied 190 DMPK alleles, on blood samples from to ninety-five subjects, previously genotyped by traditional methods to validate a new assay. The pedigree of a DM1 family was used to expand our analysis. Results: TP-PCR assay correctly identified all 95/95 (100{\%}) subjects and these results were in agreement with the other molecular laboratory. By conventional methods the amplification failure due to allele dropout in our cohort was in 12/190 (6.3{\%}) DMPK alleles analyzed. When these 12 alleles were detected and solved by new assay, we found that the 2.6{\%} was caused by primer sequence-dependent and the remaining 3.6{\%} by polymerase-hindering secondary structures. Conclusions: Allele dropout could be considered as a potentially important problem in DM1 diagnosis that may lead to the attribution of a wrong genotype with long-term consequences for both proband and family.",
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AU - De Siena, Claudia

AU - Cardani, Rosanna

AU - Brigonzi, Elisa

AU - Bosè, Francesca

AU - Fossati, Barbara

AU - Meola, Giovanni

AU - Costa, Elena

AU - Valaperta, Rea

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N2 - Background: Myotonic dystrophy type 1 (DM1) is caused by an expanded CTG repeat in the non-coding 3’ UTR of the DMPK gene. PCR and Southern Blot Analysis (SBA) of long-range PCR represent the routine molecular testing most widely used for DM1 diagnosis. However, in these conventional methods artifacts such as allele dropout (ADO) represent a risk of misdiagnosis for DM1. Subjects, who show a single product by conventional methods, require a complementary technique such as triplet repeat primed PCR (TP-PCR). Object: To estimate and minimize the incidence of allele dropout event in our diagnostic molecular laboratory by the use of new kit TP-PCR-based. Methods: We retrospectively studied 190 DMPK alleles, on blood samples from to ninety-five subjects, previously genotyped by traditional methods to validate a new assay. The pedigree of a DM1 family was used to expand our analysis. Results: TP-PCR assay correctly identified all 95/95 (100%) subjects and these results were in agreement with the other molecular laboratory. By conventional methods the amplification failure due to allele dropout in our cohort was in 12/190 (6.3%) DMPK alleles analyzed. When these 12 alleles were detected and solved by new assay, we found that the 2.6% was caused by primer sequence-dependent and the remaining 3.6% by polymerase-hindering secondary structures. Conclusions: Allele dropout could be considered as a potentially important problem in DM1 diagnosis that may lead to the attribution of a wrong genotype with long-term consequences for both proband and family.

AB - Background: Myotonic dystrophy type 1 (DM1) is caused by an expanded CTG repeat in the non-coding 3’ UTR of the DMPK gene. PCR and Southern Blot Analysis (SBA) of long-range PCR represent the routine molecular testing most widely used for DM1 diagnosis. However, in these conventional methods artifacts such as allele dropout (ADO) represent a risk of misdiagnosis for DM1. Subjects, who show a single product by conventional methods, require a complementary technique such as triplet repeat primed PCR (TP-PCR). Object: To estimate and minimize the incidence of allele dropout event in our diagnostic molecular laboratory by the use of new kit TP-PCR-based. Methods: We retrospectively studied 190 DMPK alleles, on blood samples from to ninety-five subjects, previously genotyped by traditional methods to validate a new assay. The pedigree of a DM1 family was used to expand our analysis. Results: TP-PCR assay correctly identified all 95/95 (100%) subjects and these results were in agreement with the other molecular laboratory. By conventional methods the amplification failure due to allele dropout in our cohort was in 12/190 (6.3%) DMPK alleles analyzed. When these 12 alleles were detected and solved by new assay, we found that the 2.6% was caused by primer sequence-dependent and the remaining 3.6% by polymerase-hindering secondary structures. Conclusions: Allele dropout could be considered as a potentially important problem in DM1 diagnosis that may lead to the attribution of a wrong genotype with long-term consequences for both proband and family.

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