Diagnosing Smith-Magenis syndrome and duplication 17p11.2 syndrome by RAI1 gene copy number variation using quantitative real-time PCR

Hoa T. Truong, Sara Solaymani-Kohal, Kevin R. Baker, Santhosh Girirajan, Stephen R. Williams, Christopher N. Vlangos, Ann C.M. Smith, David J. Bunyan, Paul E. Roffey, Christopher L. Blanchard, Sarah H. Elsea

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Smith-Magenis syndrome (SMS) and duplication 17p11.2 (dup17p11.2) syndrome are multiple congenital anomalies/mental retardation disorders resulting from either a deletion or duplication of the 17p11.2 region, respectively. The retinoic acid induced 1 (RAI1) gene is the causative gene for SMS and is included in the 17p11.2 region of dup17p11.2 syndrome. Currently SMS and dup17p11.2 syndrome are diagnosed using a combination of clinically recognized phenotypes and molecular cytogenetic analyses such as fluorescent in situ hybridization (FISH). However, these methods have proven to be highly expensive, time consuming, and dependent upon the low resolving capabilities of the assay. To address the need for improved diagnostic methods for SMS and dup17p11.2 syndrome, we designed a quantitative real-time PCR (Q-PCR) assay that measures RAI1 copy number using the comparative Ct method, ΔΔCt. We tested our assay with samples blinded to their previous SMS or dup17p11.2 syndrome status. In all cases, we were able to determine RAI1 copy number status and render a correct diagnosis accordingly. We validated these results by both FISH and multiplex ligation-dependent probe amplification (MLPA). We conclude that Q-PCR is an accurate, reproducible, low-cost, and reliable assay that can be employed for routine use in SMS and dup17p11.2 diagnosis.

Original languageEnglish (US)
Pages (from-to)67-73
Number of pages7
JournalGenetic Testing
Volume12
Issue number1
DOIs
StatePublished - Mar 1 2008

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Smith-Magenis Syndrome
Gene Dosage
Tretinoin
Real-Time Polymerase Chain Reaction
Fluorescence In Situ Hybridization
Cytogenetic Analysis
Multiplex Polymerase Chain Reaction
Mental Disorders
Intellectual Disability
Genes
Potocki-Lupski syndrome
Phenotype
Costs and Cost Analysis

All Science Journal Classification (ASJC) codes

  • Genetics(clinical)

Cite this

Truong, Hoa T. ; Solaymani-Kohal, Sara ; Baker, Kevin R. ; Girirajan, Santhosh ; Williams, Stephen R. ; Vlangos, Christopher N. ; Smith, Ann C.M. ; Bunyan, David J. ; Roffey, Paul E. ; Blanchard, Christopher L. ; Elsea, Sarah H. / Diagnosing Smith-Magenis syndrome and duplication 17p11.2 syndrome by RAI1 gene copy number variation using quantitative real-time PCR. In: Genetic Testing. 2008 ; Vol. 12, No. 1. pp. 67-73.
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abstract = "Smith-Magenis syndrome (SMS) and duplication 17p11.2 (dup17p11.2) syndrome are multiple congenital anomalies/mental retardation disorders resulting from either a deletion or duplication of the 17p11.2 region, respectively. The retinoic acid induced 1 (RAI1) gene is the causative gene for SMS and is included in the 17p11.2 region of dup17p11.2 syndrome. Currently SMS and dup17p11.2 syndrome are diagnosed using a combination of clinically recognized phenotypes and molecular cytogenetic analyses such as fluorescent in situ hybridization (FISH). However, these methods have proven to be highly expensive, time consuming, and dependent upon the low resolving capabilities of the assay. To address the need for improved diagnostic methods for SMS and dup17p11.2 syndrome, we designed a quantitative real-time PCR (Q-PCR) assay that measures RAI1 copy number using the comparative Ct method, ΔΔCt. We tested our assay with samples blinded to their previous SMS or dup17p11.2 syndrome status. In all cases, we were able to determine RAI1 copy number status and render a correct diagnosis accordingly. We validated these results by both FISH and multiplex ligation-dependent probe amplification (MLPA). We conclude that Q-PCR is an accurate, reproducible, low-cost, and reliable assay that can be employed for routine use in SMS and dup17p11.2 diagnosis.",
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Truong, HT, Solaymani-Kohal, S, Baker, KR, Girirajan, S, Williams, SR, Vlangos, CN, Smith, ACM, Bunyan, DJ, Roffey, PE, Blanchard, CL & Elsea, SH 2008, 'Diagnosing Smith-Magenis syndrome and duplication 17p11.2 syndrome by RAI1 gene copy number variation using quantitative real-time PCR', Genetic Testing, vol. 12, no. 1, pp. 67-73. https://doi.org/10.1089/gte.2007.0058

Diagnosing Smith-Magenis syndrome and duplication 17p11.2 syndrome by RAI1 gene copy number variation using quantitative real-time PCR. / Truong, Hoa T.; Solaymani-Kohal, Sara; Baker, Kevin R.; Girirajan, Santhosh; Williams, Stephen R.; Vlangos, Christopher N.; Smith, Ann C.M.; Bunyan, David J.; Roffey, Paul E.; Blanchard, Christopher L.; Elsea, Sarah H.

In: Genetic Testing, Vol. 12, No. 1, 01.03.2008, p. 67-73.

Research output: Contribution to journalArticle

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T1 - Diagnosing Smith-Magenis syndrome and duplication 17p11.2 syndrome by RAI1 gene copy number variation using quantitative real-time PCR

AU - Truong, Hoa T.

AU - Solaymani-Kohal, Sara

AU - Baker, Kevin R.

AU - Girirajan, Santhosh

AU - Williams, Stephen R.

AU - Vlangos, Christopher N.

AU - Smith, Ann C.M.

AU - Bunyan, David J.

AU - Roffey, Paul E.

AU - Blanchard, Christopher L.

AU - Elsea, Sarah H.

PY - 2008/3/1

Y1 - 2008/3/1

N2 - Smith-Magenis syndrome (SMS) and duplication 17p11.2 (dup17p11.2) syndrome are multiple congenital anomalies/mental retardation disorders resulting from either a deletion or duplication of the 17p11.2 region, respectively. The retinoic acid induced 1 (RAI1) gene is the causative gene for SMS and is included in the 17p11.2 region of dup17p11.2 syndrome. Currently SMS and dup17p11.2 syndrome are diagnosed using a combination of clinically recognized phenotypes and molecular cytogenetic analyses such as fluorescent in situ hybridization (FISH). However, these methods have proven to be highly expensive, time consuming, and dependent upon the low resolving capabilities of the assay. To address the need for improved diagnostic methods for SMS and dup17p11.2 syndrome, we designed a quantitative real-time PCR (Q-PCR) assay that measures RAI1 copy number using the comparative Ct method, ΔΔCt. We tested our assay with samples blinded to their previous SMS or dup17p11.2 syndrome status. In all cases, we were able to determine RAI1 copy number status and render a correct diagnosis accordingly. We validated these results by both FISH and multiplex ligation-dependent probe amplification (MLPA). We conclude that Q-PCR is an accurate, reproducible, low-cost, and reliable assay that can be employed for routine use in SMS and dup17p11.2 diagnosis.

AB - Smith-Magenis syndrome (SMS) and duplication 17p11.2 (dup17p11.2) syndrome are multiple congenital anomalies/mental retardation disorders resulting from either a deletion or duplication of the 17p11.2 region, respectively. The retinoic acid induced 1 (RAI1) gene is the causative gene for SMS and is included in the 17p11.2 region of dup17p11.2 syndrome. Currently SMS and dup17p11.2 syndrome are diagnosed using a combination of clinically recognized phenotypes and molecular cytogenetic analyses such as fluorescent in situ hybridization (FISH). However, these methods have proven to be highly expensive, time consuming, and dependent upon the low resolving capabilities of the assay. To address the need for improved diagnostic methods for SMS and dup17p11.2 syndrome, we designed a quantitative real-time PCR (Q-PCR) assay that measures RAI1 copy number using the comparative Ct method, ΔΔCt. We tested our assay with samples blinded to their previous SMS or dup17p11.2 syndrome status. In all cases, we were able to determine RAI1 copy number status and render a correct diagnosis accordingly. We validated these results by both FISH and multiplex ligation-dependent probe amplification (MLPA). We conclude that Q-PCR is an accurate, reproducible, low-cost, and reliable assay that can be employed for routine use in SMS and dup17p11.2 diagnosis.

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