Detection of low-prevalence somatic TSC2 mutations in sporadic pulmonary lymphangioleiomyomatosis tissues by deep sequencing View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2016-01

AUTHORS

Atsushi Fujita, Katsutoshi Ando, Etsuko Kobayashi, Keiko Mitani, Koji Okudera, Mitsuko Nakashima, Satoko Miyatake, Yoshinori Tsurusaki, Hirotomo Saitsu, Kuniaki Seyama, Noriko Miyake, Naomichi Matsumoto

ABSTRACT

Lymphangioleiomyomatosis (LAM) (MIM #606690) is a rare lung disorder leading to respiratory failure associated with progressive cystic destruction due to the proliferation and infiltration of abnormal smooth muscle-like cells (LAM cells). LAM can occur alone (sporadic LAM, S-LAM) or combined with tuberous sclerosis complex (TSC-LAM). TSC is caused by a germline heterozygous mutation in either TSC1 or TSC2, and TSC-LAM is thought to occur as a result of a somatic mutation (second hit) in addition to a germline mutation in TSC1 or TSC2 (first hit). S-LAM is also thought to occur under the two-hit model involving a somatic mutation and/or loss of heterozygosity in TSC2. To identify TSC1 or TSC2 changes in S-LAM patients, the two genes were analyzed by deep next-generation sequencing (NGS) using genomic DNA from blood leukocytes (n = 9), LAM tissue from lung (n = 7), LAM cultured cells (n = 4), or LAM cell clusters (n = 1). We identified nine somatic mutations in six of nine S-LAM patients (67 %) with mutant allele frequencies of 1.7-46.2 %. Three of these six patients (50 %) showed two different TSC2 mutations with allele frequencies of 1.7-28.7 %. Furthermore, at least five mutations with low prevalence (<20 % of allele frequency) were confirmed by droplet digital PCR. As LAM tissues are likely to be composed of heterogeneous cell populations, mutant allele frequencies can be low. Our results confirm the consistent finding of TSC2 mutations in LAM samples, and highlight the benefit of laser capture microdissection and in-depth allele analyses for detection, such as NGS. More... »

PAGES

61-68

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s00439-015-1611-0

DOI

http://dx.doi.org/10.1007/s00439-015-1611-0

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1000452592

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/26563443


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    "description": "Lymphangioleiomyomatosis (LAM) (MIM #606690) is a rare lung disorder leading to respiratory failure associated with progressive cystic destruction due to the proliferation and infiltration of abnormal smooth muscle-like cells (LAM cells). LAM can occur alone (sporadic LAM, S-LAM) or combined with tuberous sclerosis complex (TSC-LAM). TSC is caused by a germline heterozygous mutation in either TSC1 or TSC2, and TSC-LAM is thought to occur as a result of a somatic mutation (second hit) in addition to a germline mutation in TSC1 or TSC2 (first hit). S-LAM is also thought to occur under the two-hit model involving a somatic mutation and/or loss of heterozygosity in TSC2. To identify TSC1 or TSC2 changes in S-LAM patients, the two genes were analyzed by deep next-generation sequencing (NGS) using genomic DNA from blood leukocytes (n\u00a0=\u00a09), LAM tissue from lung (n\u00a0=\u00a07), LAM cultured cells (n\u00a0=\u00a04), or LAM cell clusters (n\u00a0=\u00a01). We identified nine somatic mutations in six of nine S-LAM patients (67\u00a0%) with mutant allele frequencies of 1.7-46.2\u00a0%. Three of these six patients (50\u00a0%) showed two different TSC2 mutations with allele frequencies of 1.7-28.7\u00a0%. Furthermore, at least five mutations with low prevalence (<20\u00a0% of allele frequency) were confirmed by droplet digital PCR. As LAM tissues are likely to be composed of heterogeneous cell populations, mutant allele frequencies can be low. Our results confirm the consistent finding of TSC2 mutations in LAM samples, and highlight the benefit of laser capture microdissection and in-depth allele analyses for detection, such as NGS. ", 
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