Matroshka and ectopic polymorphisms: Two new classes of DNA sequence variation identified at the van der woude syndrome locus on 1q32-q41

Yoriko Watanabe, Jeffrey C. Murray, Bryan C. Bjork, Christine P. Bird, Pei-Wen Chiang, Simon G. Gregory, David M. Kurnit, Brian C. Schutte

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Van der Woude syndrome (VWS) is an orofacial clefting disorder with an autosomal dominant pattern of inheritance. In our efforts to clone the VWS gene, 900 kb of genomic sequence from the VWS candidate region at chromosome 1q32-q41 was analyzed for new DNA sequence variants. We observed that in clone CTA-321i20 a 7922 bp sequence is absent relative to the sequence present in PAC clone RP4-782d21 at positions 1669-9590, suggesting the presence of a deletion/insertion (del/ins) polymorphism. Embedded in this 7922 bp region was a TTCC short tandem repeat (STR). Genotype analysis showed that both the internal STR and the (del/ins) mutation were true polymorphisms. This is a novel example of intraallelic variation, a polymorphism within a polymorphism, and we suggest that it be termed a "Matroshka" polymorphism. Further genetic and DNA sequence analysis indicated that the ancestral state of the 1669-9590 del/ins polymorphism was the insertion allele and that the original deletion mutation probably occurred only once. A second class of novel DNA sequence variation was discovered on chromosome 5 that shared a 328 bp identical sequence with this region on chromosome 1. A single nucleotide polymorphism (SNP) was detected by SSCP using a pair of primers derived from the chromosome 1 sequence. Surprisingly, these primers also amplified the identical locus on chromosome 5, and the SNP was only located on chromosome 5. Since the probe unexpectedly detected alleles from another locus, we suggest that this type of sequence variant be termed an "ectopic" polymorphism. These two novel classes of DNA sequence polymorphisms have the potential to confound genetic and DNA sequence analysis and may also contribute to variation in disease phenotypes.

Original languageEnglish (US)
Pages (from-to)422-434
Number of pages13
JournalHuman Mutation
Volume18
Issue number5
DOIs
StatePublished - 2001
Externally publishedYes

Fingerprint

Chromosomes, Human, Pair 5
Clone Cells
Chromosomes, Human, Pair 1
DNA Sequence Analysis
Microsatellite Repeats
Single Nucleotide Polymorphism
INDEL Mutation
Alleles
Single-Stranded Conformational Polymorphism
Inheritance Patterns
Sequence Deletion
Chromosomes
Genotype
Phenotype
Genes
Van der Woude syndrome

Keywords

  • Ancient mutation
  • Deletion/insertion
  • Ectopic polymorphism
  • Linkage disequilibrium
  • Matroshka polymorphism
  • Quantitative PCR
  • STR
  • Van der Woude syndrome
  • VWS

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Watanabe, Y., Murray, J. C., Bjork, B. C., Bird, C. P., Chiang, P-W., Gregory, S. G., ... Schutte, B. C. (2001). Matroshka and ectopic polymorphisms: Two new classes of DNA sequence variation identified at the van der woude syndrome locus on 1q32-q41. Human Mutation, 18(5), 422-434. https://doi.org/10.1002/humu.1213

Matroshka and ectopic polymorphisms : Two new classes of DNA sequence variation identified at the van der woude syndrome locus on 1q32-q41. / Watanabe, Yoriko; Murray, Jeffrey C.; Bjork, Bryan C.; Bird, Christine P.; Chiang, Pei-Wen; Gregory, Simon G.; Kurnit, David M.; Schutte, Brian C.

In: Human Mutation, Vol. 18, No. 5, 2001, p. 422-434.

Research output: Contribution to journalArticle

Watanabe, Y, Murray, JC, Bjork, BC, Bird, CP, Chiang, P-W, Gregory, SG, Kurnit, DM & Schutte, BC 2001, 'Matroshka and ectopic polymorphisms: Two new classes of DNA sequence variation identified at the van der woude syndrome locus on 1q32-q41', Human Mutation, vol. 18, no. 5, pp. 422-434. https://doi.org/10.1002/humu.1213
Watanabe, Yoriko ; Murray, Jeffrey C. ; Bjork, Bryan C. ; Bird, Christine P. ; Chiang, Pei-Wen ; Gregory, Simon G. ; Kurnit, David M. ; Schutte, Brian C. / Matroshka and ectopic polymorphisms : Two new classes of DNA sequence variation identified at the van der woude syndrome locus on 1q32-q41. In: Human Mutation. 2001 ; Vol. 18, No. 5. pp. 422-434.
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abstract = "Van der Woude syndrome (VWS) is an orofacial clefting disorder with an autosomal dominant pattern of inheritance. In our efforts to clone the VWS gene, 900 kb of genomic sequence from the VWS candidate region at chromosome 1q32-q41 was analyzed for new DNA sequence variants. We observed that in clone CTA-321i20 a 7922 bp sequence is absent relative to the sequence present in PAC clone RP4-782d21 at positions 1669-9590, suggesting the presence of a deletion/insertion (del/ins) polymorphism. Embedded in this 7922 bp region was a TTCC short tandem repeat (STR). Genotype analysis showed that both the internal STR and the (del/ins) mutation were true polymorphisms. This is a novel example of intraallelic variation, a polymorphism within a polymorphism, and we suggest that it be termed a {"}Matroshka{"} polymorphism. Further genetic and DNA sequence analysis indicated that the ancestral state of the 1669-9590 del/ins polymorphism was the insertion allele and that the original deletion mutation probably occurred only once. A second class of novel DNA sequence variation was discovered on chromosome 5 that shared a 328 bp identical sequence with this region on chromosome 1. A single nucleotide polymorphism (SNP) was detected by SSCP using a pair of primers derived from the chromosome 1 sequence. Surprisingly, these primers also amplified the identical locus on chromosome 5, and the SNP was only located on chromosome 5. Since the probe unexpectedly detected alleles from another locus, we suggest that this type of sequence variant be termed an {"}ectopic{"} polymorphism. These two novel classes of DNA sequence polymorphisms have the potential to confound genetic and DNA sequence analysis and may also contribute to variation in disease phenotypes.",
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