The Suitability of Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry in a Laboratory Developed Test Using Cystic Fibrosis Carrier Screening as a Model

Farkas, Daniel H.; Miltgen, Nicholas E.; Stoerker, Jay; Boom, Dirk van den; Highsmith, W. Edward; Cagasan, Lesley; McCullough, Ron; Mueller, Reinhold; Tang, Lin; Tynan, John A.; Tate, Courtney M.; Bombard, Allan T.

doi:10.2353/jmoldx.2010.090233

Cited by 15 publications

(10 citation statements)

References 19 publications

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“…The diagnostic accuracy of the OpenArray was higher than the Dynamic Array [23] and other methods such as MALDI-TOF mass spectrometry [10]. The overall throughput for the two platforms tested ranges from approximately 55,000–70,000 genotypes per day on one instrument, which is comparable if not higher than other platforms.…”

Section: Discussionmentioning

confidence: 85%

“…Methods such as Restriction Fragment Length Polymorphism (RFLP) testing [8] or the Amplification Refractory Mutation System (ARMS) [9], however, are hindered by time-consuming gel-based evaluation of PCR amplicons. Additionally, the platforms that have been developed for high-throughput genotyping purposes, such as a PCR and matrix-assisted, laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry method [10] or arrayed primer extension (APEX) [11], are labor-intensive. Therefore, a more efficient, high-throughput, and automated method of screening for common mutations is needed.…”

Section: Introductionmentioning

confidence: 99%

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High-Throughput Carrier Screening Using TaqMan Allelic Discrimination

Fedick

Jalas

et al. 2013

PLoS ONE

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Members of the Ashkenazi Jewish community are at an increased risk for inheritance of numerous genetic diseases such that carrier screening is medically recommended. This paper describes the development and evaluation of 30 TaqMan allelic discrimination qPCR assays for 29 mutations on 2 different high-throughput platforms. Four of these mutations are in the GBA gene and are successfully examined using short amplicons due to the qualitative nature of TaqMan allelic discrimination. Two systems were tested for their reliability (call rate) and consistency with previous diagnoses (diagnostic accuracy) indicating a call rate of 99.04% and a diagnostic accuracy of 100% (+/−0.00%) from one platform, and a call rate of 94.66% and a diagnostic accuracy of 93.35% (+/−0.29%) from a second for 9,216 genotypes. Results for mutations tested at the expected carrier frequency indicated a call rate of 97.87% and a diagnostic accuracy of 99.96% (+/−0.05%). This study demonstrated the ability of a high throughput qPCR methodology to accurately and reliably genotype 29 mutations in parallel. The universally applicable nature of this technology provides an opportunity to increase the number of mutations that can be screened simultaneously, and reduce the cost and turnaround time for accommodating newly identified and clinically relevant mutations.

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Section: Discussionmentioning

confidence: 85%

Section: Introductionmentioning

confidence: 99%

High-Throughput Carrier Screening Using TaqMan Allelic Discrimination

Fedick

Jalas

et al. 2013

PLoS ONE

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“…MS analysis uses at least an order of magnitude less DNA (o10 ng), with much higher throughput and greater sensitivity and accuracy. 34,35 The inclusion of a primer extension step after PCR also increases precision and accommodates DNA samples of poorer quality. Therefore, the MALDI-TOF approach could provide greater precision with fewer assays than direct sequencing and useful to examine allele frequencies in a large number of samples.…”

Section: Discussionmentioning

confidence: 99%

Estimation of carrier frequencies of six autosomal-recessive Mendelian disorders in the Korean population

Song

Lee

et al. 2011

J Hum Genet

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Although many studies have been performed to identify mutations in Korean patients with various autosomal-recessive Mendelian disorders (AR-MDs), little is known about the carrier frequencies of AR-MDs in the Korean population. Twenty common mutations from six AR-MDs, including Wilson disease (WD), non-syndromic hearing loss (NSHL), glycogen storage disease type Ia (GSD Ia), phenylketonuria (PKU), congenital hypothyroidism (CH), and congenital lipoid adrenal hyperplasia (CLAH) were selected to screen for based on previous studies. A total of 3057 Koreans were genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry followed by confirmation using the Sanger sequencing. We found 201 and 8 carriers with either one or two mutations in different genes, respectively, yielding a total carrier frequency of 1 in 15 (6.7%). Of the six AR-MDs, NSHL has the highest carrier frequency followed by WD, CH, CLAH, GSD Ia, and PKU. As carrier screening tests are becoming prevalent and the number of mutations known and tested is rising, a priori data on the carrier frequencies in different ethnic groups is mandatory to plan a population screening program and to estimate its efficiency. In light of this, the present results can be used as a basis to establish a screening policy for common AR-MRs in the Korean population.

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“…Blinded samples were sent to aMDx with 50 of the patient samples removed at random and replaced with DNA at a similar concentration and volume with control DNA samples from Coriell. Before analysis of the data by White Crow, definitions for the comparison were established as proposed by Farkas et al 6 Table 3. For the 450 samples analyzed by the authority laboratory (or the Coriell Cell Repository) and the aMDx test, all samples were concordant.…”

Section: Resultsmentioning

confidence: 99%

Evaluation of a BeadXpress Assay for a 151-Mutation and Variant CFTR Screening Panel After 11,000 Samples

Stoerker¹,

Goodman²,

Walline³

et al. 2013

Diagnostic Molecular Pathology

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We created a 151-mutation and variant screening panel for cystic fibrosis transmembrane regulator (CFTR) using the Illumina Inc. BeadXpress platform (San Diego, CA). The laboratory developed test was validated using a third-party blinding of a set of 450 samples split with an authority laboratory that provides a large panel CFTR screening and 50 diverse controls admixed randomly. The validation proved the test to be 100% sensitive for the mutations tested and >99% specific. A total of 391 mutations in 11,186 samples tested were confirmed by repeat analysis and sequencing, resulting in an overall confirmed positive rate of 3.5%. Of the mutations detected, 348 were part of the American College of Obstetrics and Gynecology (ACOG) panel (89%) and 43 were non-ACOG (11%). A total of 16 of the 23 ACOG panel mutations were discovered in this cohort, along with 21 different non-ACOG mutation genotypes. We confirmed 6 total patients carrying mutations that would not have been identified by any other commercial panel. The role of a large genotyping panel in carrier screening is discussed relative to the ACOG panel and also in relation to comparative efficacy with targeted massive parallel sequencing.

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The Suitability of Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry in a Laboratory Developed Test Using Cystic Fibrosis Carrier Screening as a Model

Cited by 15 publications

References 19 publications

High-Throughput Carrier Screening Using TaqMan Allelic Discrimination

High-Throughput Carrier Screening Using TaqMan Allelic Discrimination

Estimation of carrier frequencies of six autosomal-recessive Mendelian disorders in the Korean population

Evaluation of a BeadXpress Assay for a 151-Mutation and Variant CFTR Screening Panel After 11,000 Samples

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