Molecular and clinical analyses of 16q24.1 duplications involving identify an evolutionarily unstable large minisatellite

Avinash V. Dharmadhikari, Tomasz Gambin, Przemyslaw Szafranski, Wenjian Cao, Frank J. Probst, Weihong Jin, Ping Fang, Krzysztof Gogolewski, Anna Gambin, Jaya K. George-Abraham, Sailaja Golla, Francoise Boidein, Benedicte Duban-Bedu, Bruno Delobel, Joris Andrieux, Kerstin Becker, Elke Holinski-Feder, Sau Wai Cheung, Pawel Stankiewicz

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Background: Point mutations or genomic deletions of result in a lethal developmental lung disease Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins. However, the clinical consequences of the constitutively increased dosage of are unknown. Methods: Copy-number variations and their parental origin were identified using a combination of array CGH, long-range PCR, DNA sequencing, and microsatellite analyses. Minisatellite sequences across different species were compared using a gready clustering algorithm and genome-wide analysis of the distribution of minisatellite sequences was performed using R statistical software. Results: We report four unrelated families with 16q24.1 duplications encompassing entire . In a 4-year-old boy with speech delay and a café-au-lait macule, we identified an ~15 kb 16q24.1 duplication inherited from the reportedly healthy father, in addition to a ~1.09 Mb mosaic 17q11.2 deletion. In a 13-year-old patient with autism and mood disorder, we found an ~0.3 Mb duplication harboring and an ~0.5 Mb 16q23.3 duplication, both inherited from the father with bipolar disorder. In a 47-year old patient with pyloric stenosis, mesenterium commune, and aplasia of the appendix, we identified an ~0.4 Mb duplication in 16q24.1 encompassing 16 genes including . The patient transmitted the duplication to her daughter, who presented with similar symptoms. In a fourth patient with speech and motor delay, and borderline intellectual disability, we identified an ~1.7 Mb duplication adjacent to a large minisatellite. This duplication has a complex structure and arose on the maternal chromosome, likely as a result of a DNA replication error initiated by the adjacent large tandem repeat. Using bioinformatic and array CGH analyses of the minisatellite, we found a large variation of its size in several different species and individuals, demonstrating both its evolutionarily instability and population polymorphism. Conclusions: Our data indicate that constitutional duplication of in humans is not associated with any pediatric lung abnormalities. We propose that patients with gut malrotation, pyloric or duodenal stenosis, and gall bladder agenesis should be tested for alterations. We suggest that instability of minisatellites greater than 1 kb can lead to structural variation due to DNA replication errors.

Original languageEnglish (US)
Article number128
JournalBMC Medical Genetics
Volume15
Issue number1
DOIs
StatePublished - Dec 4 2014

Fingerprint

Minisatellite Repeats
Pyloric Stenosis
Language Development Disorders
DNA Replication
Fathers
Persistent Fetal Circulation Syndrome
Tandem Repeat Sequences
Autistic Disorder
Computational Biology
Nuclear Family
Mood Disorders
DNA Sequence Analysis
Bipolar Disorder
Point Mutation
Intellectual Disability
Microsatellite Repeats
Lung Diseases
Cluster Analysis
Urinary Bladder
Software

Keywords

  • cis-regulation
  • Microduplication
  • Microhomology-mediated break-induced replication
  • Satellite repeats

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Dharmadhikari, A. V., Gambin, T., Szafranski, P., Cao, W., Probst, F. J., Jin, W., ... Stankiewicz, P. (2014). Molecular and clinical analyses of 16q24.1 duplications involving identify an evolutionarily unstable large minisatellite. BMC Medical Genetics, 15(1), [128]. https://doi.org/10.1186/s12881-014-0128-z

Molecular and clinical analyses of 16q24.1 duplications involving identify an evolutionarily unstable large minisatellite. / Dharmadhikari, Avinash V.; Gambin, Tomasz; Szafranski, Przemyslaw; Cao, Wenjian; Probst, Frank J.; Jin, Weihong; Fang, Ping; Gogolewski, Krzysztof; Gambin, Anna; George-Abraham, Jaya K.; Golla, Sailaja; Boidein, Francoise; Duban-Bedu, Benedicte; Delobel, Bruno; Andrieux, Joris; Becker, Kerstin; Holinski-Feder, Elke; Cheung, Sau Wai; Stankiewicz, Pawel.

In: BMC Medical Genetics, Vol. 15, No. 1, 128, 04.12.2014.

Research output: Contribution to journalArticle

Dharmadhikari, AV, Gambin, T, Szafranski, P, Cao, W, Probst, FJ, Jin, W, Fang, P, Gogolewski, K, Gambin, A, George-Abraham, JK, Golla, S, Boidein, F, Duban-Bedu, B, Delobel, B, Andrieux, J, Becker, K, Holinski-Feder, E, Cheung, SW & Stankiewicz, P 2014, 'Molecular and clinical analyses of 16q24.1 duplications involving identify an evolutionarily unstable large minisatellite', BMC Medical Genetics, vol. 15, no. 1, 128. https://doi.org/10.1186/s12881-014-0128-z
Dharmadhikari, Avinash V. ; Gambin, Tomasz ; Szafranski, Przemyslaw ; Cao, Wenjian ; Probst, Frank J. ; Jin, Weihong ; Fang, Ping ; Gogolewski, Krzysztof ; Gambin, Anna ; George-Abraham, Jaya K. ; Golla, Sailaja ; Boidein, Francoise ; Duban-Bedu, Benedicte ; Delobel, Bruno ; Andrieux, Joris ; Becker, Kerstin ; Holinski-Feder, Elke ; Cheung, Sau Wai ; Stankiewicz, Pawel. / Molecular and clinical analyses of 16q24.1 duplications involving identify an evolutionarily unstable large minisatellite. In: BMC Medical Genetics. 2014 ; Vol. 15, No. 1.
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abstract = "Background: Point mutations or genomic deletions of result in a lethal developmental lung disease Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins. However, the clinical consequences of the constitutively increased dosage of are unknown. Methods: Copy-number variations and their parental origin were identified using a combination of array CGH, long-range PCR, DNA sequencing, and microsatellite analyses. Minisatellite sequences across different species were compared using a gready clustering algorithm and genome-wide analysis of the distribution of minisatellite sequences was performed using R statistical software. Results: We report four unrelated families with 16q24.1 duplications encompassing entire . In a 4-year-old boy with speech delay and a caf{\'e}-au-lait macule, we identified an ~15 kb 16q24.1 duplication inherited from the reportedly healthy father, in addition to a ~1.09 Mb mosaic 17q11.2 deletion. In a 13-year-old patient with autism and mood disorder, we found an ~0.3 Mb duplication harboring and an ~0.5 Mb 16q23.3 duplication, both inherited from the father with bipolar disorder. In a 47-year old patient with pyloric stenosis, mesenterium commune, and aplasia of the appendix, we identified an ~0.4 Mb duplication in 16q24.1 encompassing 16 genes including . The patient transmitted the duplication to her daughter, who presented with similar symptoms. In a fourth patient with speech and motor delay, and borderline intellectual disability, we identified an ~1.7 Mb duplication adjacent to a large minisatellite. This duplication has a complex structure and arose on the maternal chromosome, likely as a result of a DNA replication error initiated by the adjacent large tandem repeat. Using bioinformatic and array CGH analyses of the minisatellite, we found a large variation of its size in several different species and individuals, demonstrating both its evolutionarily instability and population polymorphism. Conclusions: Our data indicate that constitutional duplication of in humans is not associated with any pediatric lung abnormalities. We propose that patients with gut malrotation, pyloric or duodenal stenosis, and gall bladder agenesis should be tested for alterations. We suggest that instability of minisatellites greater than 1 kb can lead to structural variation due to DNA replication errors.",
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AU - Dharmadhikari, Avinash V.

AU - Gambin, Tomasz

AU - Szafranski, Przemyslaw

AU - Cao, Wenjian

AU - Probst, Frank J.

AU - Jin, Weihong

AU - Fang, Ping

AU - Gogolewski, Krzysztof

AU - Gambin, Anna

AU - George-Abraham, Jaya K.

AU - Golla, Sailaja

AU - Boidein, Francoise

AU - Duban-Bedu, Benedicte

AU - Delobel, Bruno

AU - Andrieux, Joris

AU - Becker, Kerstin

AU - Holinski-Feder, Elke

AU - Cheung, Sau Wai

AU - Stankiewicz, Pawel

PY - 2014/12/4

Y1 - 2014/12/4

N2 - Background: Point mutations or genomic deletions of result in a lethal developmental lung disease Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins. However, the clinical consequences of the constitutively increased dosage of are unknown. Methods: Copy-number variations and their parental origin were identified using a combination of array CGH, long-range PCR, DNA sequencing, and microsatellite analyses. Minisatellite sequences across different species were compared using a gready clustering algorithm and genome-wide analysis of the distribution of minisatellite sequences was performed using R statistical software. Results: We report four unrelated families with 16q24.1 duplications encompassing entire . In a 4-year-old boy with speech delay and a café-au-lait macule, we identified an ~15 kb 16q24.1 duplication inherited from the reportedly healthy father, in addition to a ~1.09 Mb mosaic 17q11.2 deletion. In a 13-year-old patient with autism and mood disorder, we found an ~0.3 Mb duplication harboring and an ~0.5 Mb 16q23.3 duplication, both inherited from the father with bipolar disorder. In a 47-year old patient with pyloric stenosis, mesenterium commune, and aplasia of the appendix, we identified an ~0.4 Mb duplication in 16q24.1 encompassing 16 genes including . The patient transmitted the duplication to her daughter, who presented with similar symptoms. In a fourth patient with speech and motor delay, and borderline intellectual disability, we identified an ~1.7 Mb duplication adjacent to a large minisatellite. This duplication has a complex structure and arose on the maternal chromosome, likely as a result of a DNA replication error initiated by the adjacent large tandem repeat. Using bioinformatic and array CGH analyses of the minisatellite, we found a large variation of its size in several different species and individuals, demonstrating both its evolutionarily instability and population polymorphism. Conclusions: Our data indicate that constitutional duplication of in humans is not associated with any pediatric lung abnormalities. We propose that patients with gut malrotation, pyloric or duodenal stenosis, and gall bladder agenesis should be tested for alterations. We suggest that instability of minisatellites greater than 1 kb can lead to structural variation due to DNA replication errors.

AB - Background: Point mutations or genomic deletions of result in a lethal developmental lung disease Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins. However, the clinical consequences of the constitutively increased dosage of are unknown. Methods: Copy-number variations and their parental origin were identified using a combination of array CGH, long-range PCR, DNA sequencing, and microsatellite analyses. Minisatellite sequences across different species were compared using a gready clustering algorithm and genome-wide analysis of the distribution of minisatellite sequences was performed using R statistical software. Results: We report four unrelated families with 16q24.1 duplications encompassing entire . In a 4-year-old boy with speech delay and a café-au-lait macule, we identified an ~15 kb 16q24.1 duplication inherited from the reportedly healthy father, in addition to a ~1.09 Mb mosaic 17q11.2 deletion. In a 13-year-old patient with autism and mood disorder, we found an ~0.3 Mb duplication harboring and an ~0.5 Mb 16q23.3 duplication, both inherited from the father with bipolar disorder. In a 47-year old patient with pyloric stenosis, mesenterium commune, and aplasia of the appendix, we identified an ~0.4 Mb duplication in 16q24.1 encompassing 16 genes including . The patient transmitted the duplication to her daughter, who presented with similar symptoms. In a fourth patient with speech and motor delay, and borderline intellectual disability, we identified an ~1.7 Mb duplication adjacent to a large minisatellite. This duplication has a complex structure and arose on the maternal chromosome, likely as a result of a DNA replication error initiated by the adjacent large tandem repeat. Using bioinformatic and array CGH analyses of the minisatellite, we found a large variation of its size in several different species and individuals, demonstrating both its evolutionarily instability and population polymorphism. Conclusions: Our data indicate that constitutional duplication of in humans is not associated with any pediatric lung abnormalities. We propose that patients with gut malrotation, pyloric or duodenal stenosis, and gall bladder agenesis should be tested for alterations. We suggest that instability of minisatellites greater than 1 kb can lead to structural variation due to DNA replication errors.

KW - cis-regulation

KW - Microduplication

KW - Microhomology-mediated break-induced replication

KW - Satellite repeats

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