Mutation Spectrum of the Survival of Motor Neuron 1 and Functional Analysis of Variants in Chinese Spinal Muscular Atrophy
Proximal spinal muscular atrophy (SMA) is a common fatal autosomal recessive disorder caused by deletion or mutation of the survival of motor neuron 1 (SMN1). Here, we studied SMA molecular pathology in 653 Chinese patients and found approximately 88.2% with homozygous SMN1 exon 7 deletion and 6.3% with heterozygous exon 7 loss using multiplex ligation-dependent probe amplification. SMN1 variants were detected in 34 patients with heterozygous SMN1 loss by clone sequencing. In 27 of them, 15 variants were identified: five were unreported novel variants [c.-7_9del(p.0), p.Tyr109Cys, p.Ile249Tyrfs*16, p.Tyr272Trpfs*35, and c....
Source: Journal of Molecular Diagnostics - July 14, 2016 Category: Pathology Authors: Yu-jin Qu, Jin-li Bai, Yan-yan Cao, Hong Wang, Yu-wei Jin, Juan Du, Xiu-shan Ge, Wen-hui Zhang, Yan Li, Sheng-xi He, Fang Song Tags: Regular Article Source Type: research

Development and Validation of a Template-Independent Next-Generation Sequencing Assay for Detecting Low-Level Resistance-Associated Variants of Hepatitis C Virus
To develop hepatitis C virus (HCV) direct-acting antiviral (DAA) drugs that can treat most HCV genotypes and offer higher barriers for treatment-resistant mutations, it is important to study resistance-associated variants (RAVs). Current commercially available RAV detection assays rely on genotype- or subtype-specific template-dependent PCR amplification. These assays are limited to genotypes and subtypes that are often prevalent in developed countries because of availability of public sequence databases. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 6, 2016 Category: Pathology Authors: Bo Wei, John Kang, Miho Kibukawa, Lei Chen, Ping Qiu, Fred Lahser, Matthew Marton, Diane Levitan Tags: Technical Advance Source Type: research

Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using Molecular Inversion Probe –Based Single-Nucleotide Polymorphism Array
Gene copy number aberrations (CNAs) represent a major class of cancer-related genomic alterations that drive solid tumors. Comprehensive and sensitive detection of CNAs is challenging because of often low quality and quantity of DNA isolated from the formalin-fixed, paraffin-embedded (FFPE) solid tumor samples. Herein, in a clinical molecular diagnostic laboratory, we tested the utility and validated a molecular inversion probe-based (MIP) array to routinely screen for CNAs in solid tumors. Using low-input FFPE DNA, the array detects genome-wide CNAs with a special focus on 900 cancer-related genes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 5, 2016 Category: Pathology Authors: Rajesh R. Singh, Meenakshi Mehrotra, Hui Chen, Alaa A. Almohammedsalim, Ayesagul Sahin, Alex Bosamra, Keyur P. Patel, Mark J. Routbort, Xinyan Lu, Abraham Ronald, Bal M. Mishra, Shumaila Virani, L. Jeffrey Medeiros, Rajyalakshmi Luthra Tags: Regular Article Source Type: research

Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using Molecular Inversion Probe–Based Single-Nucleotide Polymorphism Array
Gene copy number aberrations (CNAs) represent a major class of cancer-related genomic alterations that drive solid tumors. Comprehensive and sensitive detection of CNAs is challenging because of often low quality and quantity of DNA isolated from the formalin-fixed, paraffin-embedded (FFPE) solid tumor samples. Herein, in a clinical molecular diagnostic laboratory, we tested the utility and validated a molecular inversion probe-based (MIP) array to routinely screen for CNAs in solid tumors. Using low-input FFPE DNA, the array detects genome-wide CNAs with a special focus on 900 cancer-related genes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 5, 2016 Category: Pathology Authors: Rajesh R. Singh, Meenakshi Mehrotra, Hui Chen, Alaa A. Almohammedsalim, Ayesagul Sahin, Alex Bosamra, Keyur P. Patel, Mark J. Routbort, Xinyan Lu, Abraham Ronald, Bal M. Mishra, Shumaila Virani, L. Jeffrey Medeiros, Rajyalakshmi Luthra Tags: Regular Article Source Type: research

Validation and Implementation of a Custom Next-Generation Sequencing Clinical Assay for Hematologic Malignancies
We report here the design, validation, and implementation of a comprehensive 95-gene next-generation sequencing panel targeted for hematologic malignancies that we named rapid heme panel. Rapid heme panel is amplicon based and covers hotspot regions of oncogenes and most of the coding regions of tumor suppressor genes. It is composed of 1330 amplicons and covers 175 kb of genomic sequence in total. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 1, 2016 Category: Pathology Authors: Michael J. Kluk, R. Coleman Lindsley, Jon C. Aster, Neal I. Lindeman, David Szeto, Dimity Hall, Frank C. Kuo Tags: Regular article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 1, 2016 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 1, 2016 Category: Pathology Source Type: research

Performance Characteristics and Validation of Next-Generation Sequencing for Human Leucocyte Antigen Typing
High-resolution human leukocyte antigen (HLA) matching reduces graft-versus-host disease and improves overall patient survival after hematopoietic stem cell transplant. Sanger sequencing has been the gold standard for HLA typing since 1996. However, given the increasing number of new HLA alleles identified and the complexity of the HLA genes, clinical HLA typing by Sanger sequencing requires several rounds of additional testing to provide allele-level resolution. Although next-generation sequencing (NGS) is routinely used in molecular genetics, few clinical HLA laboratories use the technology. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 1, 2016 Category: Pathology Authors: Eric T. Weimer, Maureen Montgomery, Rosanne Petraroia, John Crawford, John L. Schmitz Tags: Regular Article Source Type: research

Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis
Advances in next-generation sequencing (NGS) have facilitated parallel analysis of multiple genes enabling the implementation of cost-effective, rapid, and high-throughput methods for the molecular diagnosis of multiple genetic conditions, including the identification of BRCA1 and BRCA2 mutations in high-risk patients for hereditary breast and ovarian cancer. We clinically validated a NGS pipeline designed to replace Sanger sequencing and multiplex ligation-dependent probe amplification analysis and to facilitate detection of sequence and copy number alterations in a single test focusing on a BRCA1/BRCA2 gene analysis pane...
Source: Journal of Molecular Diagnostics - July 1, 2016 Category: Pathology Authors: Laila C. Schenkel, Jennifer Kerkhof, Alan Stuart, Jack Reilly, Barry Eng, Crystal Woodside, Alexander Levstik, Christopher J. Howlett, Anthony C. Rupar, Joan H.M. Knoll, Peter Ainsworth, John S. Waye, Bekim Sadikovic Tags: Technical Advance Source Type: research

Performance Characteristics and Validation of Next-Generation Sequencing for Human Leucocyte Antigen Typing
High-resolution human leukocyte antigen (HLA) matching reduces graft-versus-host disease and improves overall patient survival after hematopoietic stem cell transplant. Sanger sequencing has been the gold standard for HLA typing since 1996. However, given the increasing number of new HLA alleles identified and the complexity of the HLA genes, clinical HLA typing by Sanger sequencing requires several rounds of additional testing to provide allele-level resolution. Although next-generation sequencing (NGS) is routinely used in molecular genetics, few clinical HLA laboratories use the technology. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 1, 2016 Category: Pathology Authors: Eric T. Weimer, Maureen Montgomery, Rosanne Petraroia, John Crawford, John L. Schmitz Tags: Regular Article Source Type: research

Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis
Advances in next-generation sequencing (NGS) have facilitated parallel analysis of multiple genes enabling the implementation of cost-effective, rapid, and high-throughput methods for the molecular diagnosis of multiple genetic conditions, including the identification of BRCA1 and BRCA2 mutations in high-risk patients for hereditary breast and ovarian cancer. We clinically validated a NGS pipeline designed to replace Sanger sequencing and multiplex ligation-dependent probe amplification analysis and to facilitate highly sensitive and specific detection of sequence and copy number alterations in a single test focusing on a ...
Source: Journal of Molecular Diagnostics - July 1, 2016 Category: Pathology Authors: Laila C. Schenkel, Jennifer Kerkhof, Alan Stuart, Jack Reilly, Barry Eng, Crystal Woodside, Alexander Levstik, Christopher J. Howlett, Anthony C. Rupar, Joan H.M. Knoll, Peter Ainsworth, John S. Waye, Bekim Sadikovic Tags: Technical Advance Source Type: research

Reality of Single Circulating Tumor Cell Sequencing for Molecular Diagnostics in Pancreatic Cancer
To understand the potential and limitations of circulating tumor cell (CTC) sequencing in the context of molecular diagnostics, we investigated the feasibility of identifying the ubiquitous KRAS mutation in single CTCs from pancreatic cancer (PC) patients. We used the NanoVelcro/laser capture microdissection CTC platform, combined with whole genome amplification and KRAS Sanger sequencing. We assessed both our ability to obtain KRAS codon-12 coverage and the degree that allele dropout during whole genome amplification affected the detection of KRAS mutations from single CTCs. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 30, 2016 Category: Pathology Authors: Colin M. Court, Jacob S. Ankeny, Shonan Sho, Shuang Hou, Qingyu Li, Carolyn Hsieh, Min Song, Xinfang Liao, Matthew M. Rochefort, Zev Wainberg, Thomas G. Graeber, Hsian-Rong Tseng, James S. Tomlinson Tags: Regular Article Source Type: research

Defining the Performance Parameters of a Rapid Screening Tool for FMR1 CGG-Repeat Expansions Based on Direct Triplet-Primed PCR and Melt Curve Analysis
Population-based screening for CGG-repeat expansions in the fragile X mental retardation 1 (FMR1) gene that cause fragile X syndrome can now be performed more cost-effectively and simply by combining direct triplet-primed PCR (dTP-PCR) with melting curve analysis (MCA). We have now performed a detailed technical validation to define the operational parameters for achieving robust and reliable performance of the FMR1 dTP-PCR MCA assay. We compared the assay's performance on 2 real-time PCR platforms and determined its analytic sensitivity and specificity. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 30, 2016 Category: Pathology Authors: Indhu-Shree Rajan-Babu, Mulias Lian, Hai Anh Tran, Tien Truong Dang, Thi Minh Huong Le, Ngoc Minh Thanh, Caroline G. Lee, Samuel S. Chong Tags: Regular Article Source Type: research

Reality of Single Circulating Tumor Cell Sequencing for Molecular Diagnostics in Pancreatic Cancer
To understand the potential and limitations of circulating tumor cell (CTC) sequencing in the context of molecular diagnostics, we investigated the feasibility of identifying the ubiquitous KRAS mutation in single CTCs from pancreatic cancer (PC) patients. We used the NanoVelcro/laser capture microdissection CTC platform, combined with whole genome amplification and KRAS Sanger sequencing. We assessed both our ability to obtain KRAS codon-12 coverage and the degree that allele dropout during whole genome amplification affected the detection of KRAS mutations from single CTCs. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 30, 2016 Category: Pathology Authors: Colin M. Court, Jacob S. Ankeny, Shonan Sho, Shuang Hou, Qingyu Li, Carolyn Hsieh, Min Song, Xinfang Liao, Matthew M. Rochefort, Zev Wainberg, Thomas G. Graeber, Hsian-Rong Tseng, James S. Tomlinson Tags: Regular Article Source Type: research

Defining the Performance Parameters of a Rapid Screening Tool for FMR1 CGG-Repeat Expansions Based on Direct Triplet-Primed PCR and Melt Curve Analysis
Population-based screening for CGG-repeat expansions in the fragile X mental retardation 1 (FMR1) gene that cause fragile X syndrome can now be performed more cost-effectively and simply by combining direct triplet-primed PCR (dTP-PCR) with melting curve analysis (MCA). We have now performed a detailed technical validation to define the operational parameters for achieving robust and reliable performance of the FMR1 dTP-PCR MCA assay. We compared the assay's performance on 2 real-time PCR platforms and determined its analytic sensitivity and specificity. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 30, 2016 Category: Pathology Authors: Indhu-Shree Rajan-Babu, Mulias Lian, Hai Anh Tran, Tien Truong Dang, Thi Minh Huong Le, Ngoc Minh Thanh, Caroline G. Lee, Samuel S. Chong Tags: Regular Article Source Type: research

Challenges in Determining Genotypes for Pharmacogenetics in Allogeneic Hematopoietic Cell Transplant Recipients
As part of a pharmacogenetic study, paired blood and oral fluid samples were tested for the IL28B polymorphism (rs12979860) before and after hematopoietic cell transplantation (HCT) to evaluate changes in the genotype and investigate the utility of genotyping in oral fluid in HCT recipients. In 54  patients with leukemia>18 years of age, samples were collected approximately 7 days before HCT and 60 days after HCT. IL28B polymorphism testing was performed using real-time PCR with allele-specific probes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 29, 2016 Category: Pathology Authors: Loralie J. Langman, Lior Nesher, Dimpy P. Shah, Jacques M. Azzi, Elizabeth J. Shpall, Katy Rezvani, John L. Black, Roy F. Chemaly Tags: Technical Advance Source Type: research

Challenges in Determining Genotypes for Pharmacogenetics in Allogeneic Hematopoietic Cell Transplant Recipients
As part of a pharmacogenetic study, paired blood and oral fluid samples were tested for the IL28B polymorphism (rs12979860) before and after hematopoietic cell transplantation (HCT) to evaluate changes in the genotype and investigate the utility of genotyping in oral fluid in HCT recipients. In 54 patients with leukemia>18 years of age, samples were collected approximately 7 days before HCT and 60 days after HCT. IL28B polymorphism testing was performed using real-time PCR with allele-specific probes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 29, 2016 Category: Pathology Authors: Loralie J. Langman, Lior Nesher, Dimpy P. Shah, Jacques M. Azzi, Elizabeth J. Shpall, Katy Rezvani, John L. Black, Roy F. Chemaly Tags: Technical Advance Source Type: research

Validation and Implementation of a Custom Next-Generation Sequencing Clinical Assay for Hematologic Malignancies
We report here the design, validation, and implementation of a comprehensive 95-gene next-generation sequencing panel targeted for hematologic malignancies that we named rapid heme panel. Rapid heme panel is amplicon based and covers hotspot regions of oncogenes and most of the coding regions of tumor suppressor genes. It is composed of 1330 amplicons and covers 175 kb of genomic sequence in total. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 20, 2016 Category: Pathology Authors: Michael J. Kluk, R. Coleman Lindsley, Jon C. Aster, Neal I. Lindeman, David Szeto, Dimity Hall, Frank C. Kuo Tags: Regular article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 20, 2016 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 20, 2016 Category: Pathology Source Type: research

Hybridization-Induced Aggregation Technology for Practical Clinical Testing
KRAS mutations have emerged as powerful predictors of response to targeted therapies in the treatment of lung and colorectal cancers; thus, prospective KRAS genotyping is essential for appropriate treatment stratification. Conventional mutation testing technologies are not ideal for routine clinical screening, as they often involve complex, time-consuming processes and/or costly instrumentation. In response, we recently introduced a unique analytical strategy for revealing KRAS mutations, based on the allele-specific hybridization-induced aggregation (HIA) of oligonucleotide probe-conjugated microbeads. (Source: Journal of...
Source: Journal of Molecular Diagnostics - June 8, 2016 Category: Pathology Authors: Hillary S. Sloane, James P. Landers, Kimberly A. Kelly Tags: Regular article Source Type: research

Next-Generation Proficiency Testing
This commentary highlights the article by Davies et  al that demonstrates the feasibility of applying proficiency testing directly to the postsequencing analysis of next-generation sequencing data. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 25, 2016 Category: Pathology Authors: Jeremy P. Segal Tags: Commentary Source Type: research

Next-Generation Proficiency Testing
This commentary highlights the article by Davies et al that demonstrates the feasibility of applying proficiency testing directly to the postsequencing analysis of next-generation sequencing data. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 25, 2016 Category: Pathology Authors: Jeremy P. Segal Tags: Editorial Source Type: research

Accurate Sample Assignment in a Multiplexed, Ultrasensitive, High-Throughput Sequencing Assay for Minimal Residual Disease
High-throughput sequencing (HTS) (next-generation sequencing) of the rearranged Ig and T-cell receptor genes promises to be less expensive and more sensitive than current methods of monitoring minimal residual disease (MRD) in patients with acute lymphoblastic leukemia. However, the adoption of new approaches by clinical laboratories requires careful evaluation of all potential sources of error and the development of strategies to ensure the highest accuracy. Timely and efficient clinical use of HTS platforms will depend on combining multiple samples (multiplexing) in each sequencing run. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 13, 2016 Category: Pathology Authors: Jack Bartram, Edward Mountjoy, Tony Brooks, Jeremy Hancock, Helen Williamson, Gary Wright, John Moppett, Nick Goulden, Mike Hubank Tags: Regular article Source Type: research

Genome-Wide Single-Nucleotide Polymorphism Array Analysis Improves Prognostication of Acute Lymphoblastic Leukemia/Lymphoma
Chromosomal abnormalities are important for the risk stratification of acute lymphoblastic leukemia/lymphoma (ALL). However, approximately 30% of pediatric and 50% of adult patients lack abnormalities with clinical relevance by traditional cytogenetic analysis. We integrated cytogenetic, fluorescence in situ hybridization, and whole-genome single-nucleotide polymorphism array results from 60 consecutive clinical ALL cases. By cytogenetic and/or fluorescence in situ hybridization analyses, recurring abnormalities with clinical relevance were observed in 33 B-cell ALL (B-ALL), including t(9;22), hyperdiploidy, KMT2A transloc...
Source: Journal of Molecular Diagnostics - May 7, 2016 Category: Pathology Authors: Yunhong Wang, Sue Miller, Diane Roulston, Dale Bixby, Lina Shao Tags: Regular article Source Type: research

Development and Validation of a Mass Spectrometry –Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease
Mucin-1 kidney disease, previously described as medullary cystic kidney disease type 1 (MCKD1, OMIM 174000), is an autosomal dominant tubulointerstitial kidney disease recently shown to be caused by a single-base insertion within the variable number tandem repeat region of the MUC1 gene. Because of variable age of disease onset and often subtle signs and symptoms, clinical diagnosis of mucin-1 kidney disease and differentiation from other forms of hereditary kidney disease have been difficult. The causal insertion resides in a variable number tandem repeat region with high GC content, which has made detection by standard n...
Source: Journal of Molecular Diagnostics - May 6, 2016 Category: Pathology Authors: Brendan Blumenstiel, Matthew DeFelice, Ozge Birsoy, Anthony J. Bleyer, Stanislav Kmoch, Todd A. Carter, Andreas Gnirke, Kendrah Kidd, Heidi L. Rehm, Lucienne Ronco, Eric S. Lander, Stacey Gabriel, Niall J. Lennon Tags: Regular article Source Type: research

Comparative Evaluation of Four Real-Time PCR Methods for the Quantitative Detection of Epstein-Barr Virus from Whole Blood Specimens
Monitoring of Epstein-Barr virus (EBV) load in immunocompromised patients has become integral to their care. An increasing number of reagents are available for quantitative detection of EBV; however, there are little published comparative data. Four real-time PCR systems (one using laboratory-developed reagents and three using analyte-specific reagents) were compared with one another for detection of EBV from whole blood. Whole blood specimens seeded with EBV were used to determine quantitative linearity, analytical measurement range, lower limit of detection, and CV for each assay. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 6, 2016 Category: Pathology Authors: Daelynn Buelow, Yilun Sun, Li Tang, Zhengming Gu, Stanley Pounds, Randall Hayden Tags: Regular article Source Type: research

Detection of Germline Mutation in Hereditary Breast and/or Ovarian Cancers by Next-Generation Sequencing on a Four-Gene Panel
Mutation in BRCA1/BRCA2 genes accounts for 20% of familial breast cancers, 5% to 10% of which may be due to other less penetrant genes which are still incompletely studied. Herein, a four-gene panel was used to examine the prevalence of BRCA1, BRCA2, TP53, and PTEN in hereditary breast and ovarian cancers in Southern Chinese population. In this cohort, 948 high-risk breast and/or ovarian patients were recruited for genetic screening by next-generation sequencing (NGS). The performance of our NGS pipeline was evaluated with 80 Sanger-validated known mutations and eight negative cases. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 6, 2016 Category: Pathology Authors: Ava Kwong, Vivian Y. Shin, Chun H. Au, Fian B.F. Law, Dona N. Ho, Bui K. Ip, Anthony T.C. Wong, Silvia S. Lau, Rene M.Y. To, Gigi Choy, James M. Ford, Edmond S.K. Ma, Tsun L. Chan Tags: Regular article Source Type: research

The Impact on Genetic Testing of Mutational Patterns of CFTR Gene in Different Clinical Macrocategories of Cystic Fibrosis
More than 2000 sequence variations of the cystic fibrosis transmembrane conductance regulator gene are known. The marked genetic heterogeneity, poor functional characterization of the vast majority of sequence variations, and an uncertain genotype-phenotype relationship complicate the definition of mutational search strategies. We studied the effect of the marked genetic heterogeneity detected in a case series comprising 610 patients of cystic fibrosis (CF), grouped in different clinical macrocategories, on the operative characteristics of the genetic test designed to fully characterize CF patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 6, 2016 Category: Pathology Authors: Marco Lucarelli, Sabina M. Bruno, Silvia Pierandrei, Giampiero Ferraguti, Giancarlo Testino, Gessica Truglio, Roberto Strom, Serena Quattrucci Tags: Regular article Source Type: research

Development and Validation of a Mass Spectrometry –Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease
Mucin-1 kidney disease, previously described as medullary cystic kidney disease type 1 (MCKD1, OMIM 174000), is an autosomal dominant tubulointerstitial kidney disease recently shown to be caused by a single-base insertion within the variable number tandem repeat region of the MUC1 gene. Because of variable age of disease onset and often subtle signs and symptoms, clinical diagnosis of mucin-1 kidney disease and differentiation from other forms of hereditary kidney disease have been difficult. The causal insertion resides in a variable number tandem repeat region with high GC content, which has made detection by standard n...
Source: Journal of Molecular Diagnostics - May 6, 2016 Category: Pathology Authors: Brendan Blumenstiel, Matthew DeFelice, Ozge Birsoy, Anthony J. Bleyer, Stanislav Kmoch, Todd A. Carter, Andreas Gnirke, Kendrah Kidd, Heidi L. Rehm, Lucienne Ronco, Eric S. Lander, Stacey Gabriel, Niall J. Lennon Tags: Regular article Source Type: research

Development and Validation of a Mass Spectrometry–Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease
Mucin-1 kidney disease, previously described as medullary cystic kidney disease type 1 (MCKD1, OMIM 174000), is an autosomal dominant tubulointerstitial kidney disease recently shown to be caused by a single-base insertion within the variable number tandem repeat region of the MUC1 gene. Because of variable age of disease onset and often subtle signs and symptoms, clinical diagnosis of mucin-1 kidney disease and differentiation from other forms of hereditary kidney disease have been difficult. The causal insertion resides in a variable number tandem repeat region with high GC content, which has made detection by standard n...
Source: Journal of Molecular Diagnostics - May 6, 2016 Category: Pathology Authors: Brendan Blumenstiel, Matthew DeFelice, Ozge Birsoy, Anthony J. Bleyer, Stanislav Kmoch, Todd A. Carter, Andreas Gnirke, Kendrah Kidd, Heidi L. Rehm, Lucienne Ronco, Eric S. Lander, Stacey Gabriel, Niall J. Lennon Tags: Regular Article Source Type: research

Comparative Evaluation of Four Real-Time PCR Methods for the Quantitative Detection of Epstein-Barr Virus from Whole Blood Specimens
Monitoring of Epstein-Barr virus (EBV) load in immunocompromised patients has become integral to their care. An increasing number of reagents are available for quantitative detection of EBV; however, there are little published comparative data. Four real-time PCR systems (one using laboratory-developed reagents and three using analyte-specific reagents) were compared with one another for detection of EBV from whole blood. Whole blood specimens seeded with EBV were used to determine quantitative linearity, analytical measurement range, lower limit of detection, and CV for each assay. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 6, 2016 Category: Pathology Authors: Daelynn Buelow, Yilun Sun, Li Tang, Zhengming Gu, Stanley Pounds, Randall Hayden Tags: Regular Article Source Type: research

Detection of Germline Mutation in Hereditary Breast and/or Ovarian Cancers by Next-Generation Sequencing on a Four-Gene Panel
Mutation in BRCA1/BRCA2 genes accounts for 20% of familial breast cancers, 5% to 10% of which may be due to other less penetrant genes which are still incompletely studied. Herein, a four-gene panel was used to examine the prevalence of BRCA1, BRCA2, TP53, and PTEN in hereditary breast and ovarian cancers in Southern Chinese population. In this cohort, 948 high-risk breast and/or ovarian patients were recruited for genetic screening by next-generation sequencing (NGS). The performance of our NGS pipeline was evaluated with 80 Sanger-validated known mutations and eight negative cases. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 6, 2016 Category: Pathology Authors: Ava Kwong, Vivian Y. Shin, Chun Hang Au, Fian B.F. Law, Dona N. Ho, Bui K. Ip, Anthony T.C. Wong, Silvia S. Lau, Rene M.Y. To, Gigi Choy, James M. Ford, Edmond S.K. Ma, Tsun L. Chan Tags: Regular Article Source Type: research

The Impact on Genetic Testing of Mutational Patterns of CFTR Gene in Different Clinical Macrocategories of Cystic Fibrosis
More than 2000 sequence variations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene are known. The marked genetic heterogeneity, poor functional characterization of the vast majority of sequence variations, and an uncertain genotype-phenotype relationship complicate the definition of mutational search strategies. We studied the effect of the marked genetic heterogeneity detected in a case series comprising 610 patients of cystic fibrosis (CF), grouped in different clinical macrocategories, on the operative characteristics of the genetic test designed to fully characterize CF patients. (Source: Journal...
Source: Journal of Molecular Diagnostics - May 6, 2016 Category: Pathology Authors: Marco Lucarelli, Sabina M. Bruno, Silvia Pierandrei, Giampiero Ferraguti, Giancarlo Testino, Gessica Truglio, Roberto Strom, Serena Quattrucci Source Type: research

Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next-Generation Sequencing Bioinformatics and Variant Interpretation
Next-generation sequencing is becoming increasingly common in clinical laboratories worldwide and is revolutionizing clinical molecular testing. However, the large amounts of raw data produced by next-generation sequencing assays and the need for complex bioinformatics analyses present unique challenges. Proficiency testing in clinical laboratories has traditionally been designed to evaluate assays in their entirety; however, it can be alternatively applied to separate assay components. We developed and implemented a multi-institutional proficiency testing approach to directly assess custom bioinformatics and variant inter...
Source: Journal of Molecular Diagnostics - May 4, 2016 Category: Pathology Authors: Kurtis D. Davies, Midhat S. Farooqi, Mike Gruidl, Charles E. Hill, Julie Woolworth-Hirschhorn, Heather Jones, Kenneth L. Jones, Anthony Magliocco, Midori Mitui, Philip H. O'Neill, Rebecca O'Rourke, Nirali M. Patel, Dahui Qin, Erica Ramos, Michael R. Rossi Tags: Regular article Source Type: research

Driver Gene Mutations in Stools of Colorectal Carcinoma Patients Detected by Targeted Next-Generation Sequencing
Detection of driver gene mutations in stool DNA represents a promising noninvasive approach for screening colorectal cancer (CRC). Amplicon-based next-generation sequencing (NGS) is a good option to study mutations in many cancer genes simultaneously and from a low amount of DNA. Our aim was to assess the feasibility of identifying mutations in 22 cancer driver genes with Ion Torrent technology in stool DNA from a series of 65 CRC patients. The assay was successful in 80% of stool DNA samples. NGS results showed 83 mutations in cancer driver genes, 29 hotspot and 54 novel mutations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 4, 2016 Category: Pathology Authors: Gemma Armengol, Virinder K. Sarhadi, Reza Ghanbari, Masoud Doghaei-Moghaddam, Reza Ansari, Masoud Sotoudeh, Pauli Puolakkainen, Arto Kokkola, Reza Malekzadeh, Sakari Knuutila Tags: Regular article Source Type: research

A Rapid and Sensitive Next-Generation Sequencing Method to Detect RB1 Mutations Improves Care for Retinoblastoma Patients and Their Families
Retinoblastoma is a childhood eye malignancy that can lead to the loss of vision, eye(s), and sometimes life. The tumors are initiated by inactivating mutations in both alleles of the tumor-suppressor gene, RB1, or, rarely, by MYCN amplification. Timely identification of a germline RB1 mutation in blood samples or either somatic RB1 mutation or MYCN amplification in tumors is important for effective care and management of retinoblastoma patients and their families. However, current procedures to thoroughly test RB1 mutations are complicated and lengthy. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 4, 2016 Category: Pathology Authors: Wenhui L. Li, Jonathan Buckley, Pedro A. Sanchez-Lara, Dennis T. Maglinte, Lucy Viduetsky, Tatiana V. Tatarinova, Jennifer G. Aparicio, Jonathan W. Kim, Margaret Au, Dejerianne Ostrow, Thomas C. Lee, Maurice O'Gorman, Alexander Judkins, David Cobrinik, Ti Tags: Regular article Source Type: research

Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next-Generation Sequencing Bioinformatics and Variant Interpretation
Next-generation sequencing is becoming increasingly common in clinical laboratories worldwide and is revolutionizing clinical molecular testing. However, the large amounts of raw data produced by next-generation sequencing assays and need for complex bioinformatics analyses present unique challenges. Proficiency testing in clinical laboratories has traditionally been designed to evaluate assays in their entirety; however, it can be alternatively applied to separate assay components. We developed and implemented a multi-institutional proficiency testing approach to directly assess custom bioinformatics and variant interpret...
Source: Journal of Molecular Diagnostics - May 4, 2016 Category: Pathology Authors: Kurtis D. Davies, Midhat S. Farooqi, Mike Gruidl, Charles E. Hill, Julie Woolworth-Hirschhorn, Heather Jones, Kenneth L. Jones, Anthony Magliocco, Midori Mitui, Philip H. O'Neill, Rebecca O'Rourke, Nirali M. Patel, Dahui Qin, Erica Ramos, Michael R. Rossi Tags: Regular Article Source Type: research

Driver Gene Mutations in Stools of Colorectal Carcinoma Patients Detected by Targeted Next-Generation Sequencing
Detection of driver gene mutations in stool DNA represents a promising noninvasive approach for screening colorectal cancer (CRC). Amplicon-based next-generation sequencing (NGS) is a good option to study mutations in many cancer genes simultaneously and from a low amount of DNA. Our aim was to assess the feasibility of identifying mutations in 22 cancer driver genes with Ion Torrent technology in stool DNA from a series of 65 CRC patients. The assay was successful in 80% of stool DNA samples. NGS results showed 83 mutations in cancer driver genes, 29 hotspot and 54 novel mutations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 4, 2016 Category: Pathology Authors: Gemma Armengol, Virinder K. Sarhadi, Reza Ghanbari, Masoud Doghaei-Moghaddam, Reza Ansari, Masoud Sotoudeh, Pauli Puolakkainen, Arto Kokkola, Reza Malekzadeh, Sakari Knuutila Tags: Regular Article Source Type: research

A Rapid and Sensitive Next-Generation Sequencing Method to Detect RB1 Mutations Improves Care for Retinoblastoma Patients and Their Families
Retinoblastoma is a childhood eye malignancy that can lead to the loss of vision, eye(s), and sometimes life. The tumors are initiated by inactivating mutations in both alleles of the tumor-suppressor gene, RB1, or, rarely, by MYCN amplification. Timely identification of a germline RB1 mutation in blood samples or either somatic RB1 mutation or MYCN amplification in tumors is important for effective care and management of retinoblastoma patients and their families. However, current procedures to thoroughly test RB1 mutations are complicated and lengthy. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 4, 2016 Category: Pathology Authors: Wenhui L. Li, Jonathan Buckley, Pedro A. Sanchez-Lara, Dennis T. Maglinte, Lucy Viduetsky, Tatiana V. Tatarinova, Jennifer G. Aparicio, Jonathan Kim, Margaret Au, Dejerianne Ostrow, Thomas Lee, Maurice O'Gorman, Alexander Judkins, David Cobrinik, Timothy Tags: Regular Article Source Type: research

Molecular Cytogenetic Analysis of JAZF1, PHF1, and YWHAE in Endometrial Stromal Tumors
Diagnosis of endometrial stromal tumors (ESTs) can be challenging, particularly endometrial stromal sarcomas (ESSs) because of variable histologic appearance, long latency to recurrence, frequent metastases with unknown primary, and overlap with endometrial stromal nodules and undifferentiated uterine sarcomas. To enhance EST diagnosis, a break-apart strategy fluorescence in situ hybridization panel to detect JAZF1, PHF1, and YWHAE rearrangements was applied to a cohort of primary or metastatic endometrial stromal nodules, ESSs, or undifferentiated uterine sarcomas (36 cases for JAZF1, 24 of which were also assessed for PH...
Source: Journal of Molecular Diagnostics - May 3, 2016 Category: Pathology Authors: Jennelle C. Hodge, Patrick P. Bedroske, Kathryn E. Pearce, William R. Sukov Tags: Regular article Source Type: research

Molecular Cytogenetic Analysis of JAZF1, PHF1, and YWHAE in Endometrial Stromal Tumors
Diagnosis of endometrial stromal tumors (ESTs) can be challenging, particularly endometrial stromal sarcomas because of variable histologic appearance, long latency to recurrence, frequent metastases with unknown primary, and overlap with endometrial stromal nodules and undifferentiated uterine sarcomas. To enhance EST diagnosis, a break-apart strategy fluorescence in situ hybridization panel to detect JAZF1, PHF1, and YWHAE rearrangements was applied to a cohort of primary or metastatic endometrial stromal nodules, endometrial stromal sarcomas, or undifferentiated uterine sarcomas (36 cases for JAZF1, 24 of which were als...
Source: Journal of Molecular Diagnostics - May 3, 2016 Category: Pathology Authors: Jennelle C. Hodge, Patrick B. Bedroske, Kathryn E. Pearce, William R. Sukov Tags: Regular Article Source Type: research

Detection of Colorectal Cancer Using a Simplified SEPT9 Gene Methylation Assay Is a Reliable Method for Opportunistic Screening
SEPT9 gene methylation was validated as a biomarker for colorectal cancer (CRC) for>10 years and available as the Epi proColon test as an aid in CRC detection for>6 years. It was proven to be an accurate, reliable, fast, and convenient molecular test. In this opportunistic screening study, we validated a further simplified SEPT9 gene methylation assay in 1031 subjects in Chinese hospitals. The sensitivity for CRC detection was 76.6% at a specificity of 95.9%, and the results showed a satisfactory detection rate for each CRC stage, including early stages. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 28, 2016 Category: Pathology Authors: Dong Wu, Guangpeng Zhou, Peng Jin, Jiqing Zhu, Shijie Li, Qi Wu, Guiqi Wang, Jianqiu Sheng, Jianming Wang, Lele Song, Xiaoliang Han, Jiaming Qian Tags: Regular article Source Type: research

Detection of Colorectal Cancer Using a Simplified SEPT9 Gene Methylation Assay Is a Reliable Method for Opportunistic Screening
SEPT9 gene methylation was validated as a biomarker for colorectal cancer (CRC) for>10 years and available as the Epi proColon test as an aid in CRC detection for>6 years. It was proven to be an accurate, reliable, fast, and convenient molecular test. In this opportunistic screening study, we validated a further simplified SEPT9 gene methylation assay in 1031 subjects in Chinese hospitals. The sensitivity for CRC detection was 76.6% at a specificity of 95.9%, and the results showed a satisfactory detection rate for each CRC stage, including early stages. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 28, 2016 Category: Pathology Authors: Dong Wu, Guangpeng Zhou, Peng Jin, Jiqing Zhu, Shijie Li, Qi Wu, Guiqi Wang, Jianqiu Sheng, Jianming Wang, Lele Song, Xiaoliang Han, Jiaming Qian Tags: Regular Article Source Type: research

Plasmid-Based Materials as Multiplex Quality Controls and Calibrators for Clinical Next-Generation Sequencing Assays
We report an approach to provide effective multianalyte controls for next-generation sequencing assays, referred to as the control plasmid spiked-in genome (CPSG). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 20, 2016 Category: Pathology Authors: David J. Sims, Robin D. Harrington, Eric C. Polley, Thomas D. Forbes, Michele G. Mehaffey, Paul M. McGregor, Corinne E. Camalier, Kneshay N. Harper, Courtney H. Bouk, Biswajit Das, Barbara A. Conley, James H. Doroshow, P. Mickey Williams, Chih-Jian Lih Tags: Regular article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 20, 2016 Category: Pathology Source Type: research