Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations

Piotr Kozlowski, Penelope Roberts, Sandra Dabora, David Franz, John Bissler, Hope Northrup, Kit Sing Au, Ross Lazarus, Dorota Domanska-Pakiela, Katarzyna Kotulska, Sergiusz Jozwiak, David J. Kwiatkowski

Research output: Contribution to journalArticle

113 Citations (Scopus)

Abstract

Tuberous sclerosis (TSC) is an autosomal dominant disorder caused by mutations in either of two genes, TSC1 and TSC2. Point mutations and small indels account for most TSC1 and TSC2 mutations. We examined 261 TSC DNA samples (209 small-mutation-negative and 52 unscreened) for large deletion/duplication mutations using multiplex ligation-dependent probe amplification (MLPA) probe sets designed to permit interrogation of all TSC1/2 exons, as well as 15-50 kb of flanking sequence. Large deletion/duplication mutations in TSC1 and TSC2 were identified in 54 patients, of which 50 were in TSC2, and 4 were in TSC1. All but two mutations were deletions. Only 13 deletions were intragenic in TSC2, and one in TSC1, so that 39 (73%) deletions extended beyond the 5′, 3′ or both ends of TSC1 or TSC2. Mutations were identified in 24% of small-mutation-negative and 8% of unscreened samples. Eight of 54 (15%) mutations were mosaic, affecting 34-62% of cells. All intragenic mutations were confirmed by LR-PCR. Genotype/phenotype analysis showed that all (21 of 21) patients with TSC2 deletions extending 3′ into the PKD1 gene had kidney cysts. Breakpoints of intragenic deletions were randomly distributed along the TSC2 sequence, and did not preferentially involve repeat sequence elements. Our own 20-plex probe sets gave more robust performance than the 40-plex probe sets from MRC-Holland. We conclude that large deletions in TSC1 and TSC2 account for about 0.5 and 6% of mutations seen in TSC patients, respectively, and MLPA is a highly sensitive and accurate detection method, including for mosaicism.

Original languageEnglish (US)
Pages (from-to)389-400
Number of pages12
JournalHuman Genetics
Volume121
Issue number3-4
DOIs
StatePublished - May 1 2007
Externally publishedYes

Fingerprint

Multiplex Polymerase Chain Reaction
Genetic Association Studies
Mutation
Tuberous Sclerosis
Sequence Deletion
Mosaicism
Point Mutation
Netherlands
Genes
Cysts
Exons
Genotype
Phenotype
Kidney
Polymerase Chain Reaction
DNA

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations. / Kozlowski, Piotr; Roberts, Penelope; Dabora, Sandra; Franz, David; Bissler, John; Northrup, Hope; Au, Kit Sing; Lazarus, Ross; Domanska-Pakiela, Dorota; Kotulska, Katarzyna; Jozwiak, Sergiusz; Kwiatkowski, David J.

In: Human Genetics, Vol. 121, No. 3-4, 01.05.2007, p. 389-400.

Research output: Contribution to journalArticle

Kozlowski, P, Roberts, P, Dabora, S, Franz, D, Bissler, J, Northrup, H, Au, KS, Lazarus, R, Domanska-Pakiela, D, Kotulska, K, Jozwiak, S & Kwiatkowski, DJ 2007, 'Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations', Human Genetics, vol. 121, no. 3-4, pp. 389-400. https://doi.org/10.1007/s00439-006-0308-9
Kozlowski, Piotr ; Roberts, Penelope ; Dabora, Sandra ; Franz, David ; Bissler, John ; Northrup, Hope ; Au, Kit Sing ; Lazarus, Ross ; Domanska-Pakiela, Dorota ; Kotulska, Katarzyna ; Jozwiak, Sergiusz ; Kwiatkowski, David J. / Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations. In: Human Genetics. 2007 ; Vol. 121, No. 3-4. pp. 389-400.
@article{35d4c56dbc1e4848a23054ef0e0eac06,
title = "Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations",
abstract = "Tuberous sclerosis (TSC) is an autosomal dominant disorder caused by mutations in either of two genes, TSC1 and TSC2. Point mutations and small indels account for most TSC1 and TSC2 mutations. We examined 261 TSC DNA samples (209 small-mutation-negative and 52 unscreened) for large deletion/duplication mutations using multiplex ligation-dependent probe amplification (MLPA) probe sets designed to permit interrogation of all TSC1/2 exons, as well as 15-50 kb of flanking sequence. Large deletion/duplication mutations in TSC1 and TSC2 were identified in 54 patients, of which 50 were in TSC2, and 4 were in TSC1. All but two mutations were deletions. Only 13 deletions were intragenic in TSC2, and one in TSC1, so that 39 (73{\%}) deletions extended beyond the 5′, 3′ or both ends of TSC1 or TSC2. Mutations were identified in 24{\%} of small-mutation-negative and 8{\%} of unscreened samples. Eight of 54 (15{\%}) mutations were mosaic, affecting 34-62{\%} of cells. All intragenic mutations were confirmed by LR-PCR. Genotype/phenotype analysis showed that all (21 of 21) patients with TSC2 deletions extending 3′ into the PKD1 gene had kidney cysts. Breakpoints of intragenic deletions were randomly distributed along the TSC2 sequence, and did not preferentially involve repeat sequence elements. Our own 20-plex probe sets gave more robust performance than the 40-plex probe sets from MRC-Holland. We conclude that large deletions in TSC1 and TSC2 account for about 0.5 and 6{\%} of mutations seen in TSC patients, respectively, and MLPA is a highly sensitive and accurate detection method, including for mosaicism.",
author = "Piotr Kozlowski and Penelope Roberts and Sandra Dabora and David Franz and John Bissler and Hope Northrup and Au, {Kit Sing} and Ross Lazarus and Dorota Domanska-Pakiela and Katarzyna Kotulska and Sergiusz Jozwiak and Kwiatkowski, {David J.}",
year = "2007",
month = "5",
day = "1",
doi = "10.1007/s00439-006-0308-9",
language = "English (US)",
volume = "121",
pages = "389--400",
journal = "Human Genetics",
issn = "0340-6717",
publisher = "Springer Verlag",
number = "3-4",

}

TY - JOUR

T1 - Identification of 54 large deletions/duplications in TSC1 and TSC2 using MLPA, and genotype-phenotype correlations

AU - Kozlowski, Piotr

AU - Roberts, Penelope

AU - Dabora, Sandra

AU - Franz, David

AU - Bissler, John

AU - Northrup, Hope

AU - Au, Kit Sing

AU - Lazarus, Ross

AU - Domanska-Pakiela, Dorota

AU - Kotulska, Katarzyna

AU - Jozwiak, Sergiusz

AU - Kwiatkowski, David J.

PY - 2007/5/1

Y1 - 2007/5/1

N2 - Tuberous sclerosis (TSC) is an autosomal dominant disorder caused by mutations in either of two genes, TSC1 and TSC2. Point mutations and small indels account for most TSC1 and TSC2 mutations. We examined 261 TSC DNA samples (209 small-mutation-negative and 52 unscreened) for large deletion/duplication mutations using multiplex ligation-dependent probe amplification (MLPA) probe sets designed to permit interrogation of all TSC1/2 exons, as well as 15-50 kb of flanking sequence. Large deletion/duplication mutations in TSC1 and TSC2 were identified in 54 patients, of which 50 were in TSC2, and 4 were in TSC1. All but two mutations were deletions. Only 13 deletions were intragenic in TSC2, and one in TSC1, so that 39 (73%) deletions extended beyond the 5′, 3′ or both ends of TSC1 or TSC2. Mutations were identified in 24% of small-mutation-negative and 8% of unscreened samples. Eight of 54 (15%) mutations were mosaic, affecting 34-62% of cells. All intragenic mutations were confirmed by LR-PCR. Genotype/phenotype analysis showed that all (21 of 21) patients with TSC2 deletions extending 3′ into the PKD1 gene had kidney cysts. Breakpoints of intragenic deletions were randomly distributed along the TSC2 sequence, and did not preferentially involve repeat sequence elements. Our own 20-plex probe sets gave more robust performance than the 40-plex probe sets from MRC-Holland. We conclude that large deletions in TSC1 and TSC2 account for about 0.5 and 6% of mutations seen in TSC patients, respectively, and MLPA is a highly sensitive and accurate detection method, including for mosaicism.

AB - Tuberous sclerosis (TSC) is an autosomal dominant disorder caused by mutations in either of two genes, TSC1 and TSC2. Point mutations and small indels account for most TSC1 and TSC2 mutations. We examined 261 TSC DNA samples (209 small-mutation-negative and 52 unscreened) for large deletion/duplication mutations using multiplex ligation-dependent probe amplification (MLPA) probe sets designed to permit interrogation of all TSC1/2 exons, as well as 15-50 kb of flanking sequence. Large deletion/duplication mutations in TSC1 and TSC2 were identified in 54 patients, of which 50 were in TSC2, and 4 were in TSC1. All but two mutations were deletions. Only 13 deletions were intragenic in TSC2, and one in TSC1, so that 39 (73%) deletions extended beyond the 5′, 3′ or both ends of TSC1 or TSC2. Mutations were identified in 24% of small-mutation-negative and 8% of unscreened samples. Eight of 54 (15%) mutations were mosaic, affecting 34-62% of cells. All intragenic mutations were confirmed by LR-PCR. Genotype/phenotype analysis showed that all (21 of 21) patients with TSC2 deletions extending 3′ into the PKD1 gene had kidney cysts. Breakpoints of intragenic deletions were randomly distributed along the TSC2 sequence, and did not preferentially involve repeat sequence elements. Our own 20-plex probe sets gave more robust performance than the 40-plex probe sets from MRC-Holland. We conclude that large deletions in TSC1 and TSC2 account for about 0.5 and 6% of mutations seen in TSC patients, respectively, and MLPA is a highly sensitive and accurate detection method, including for mosaicism.

UR - http://www.scopus.com/inward/record.url?scp=34147099632&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34147099632&partnerID=8YFLogxK

U2 - 10.1007/s00439-006-0308-9

DO - 10.1007/s00439-006-0308-9

M3 - Article

VL - 121

SP - 389

EP - 400

JO - Human Genetics

JF - Human Genetics

SN - 0340-6717

IS - 3-4

ER -