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Topic: Diagnostic Development

Title: Development of a Novel Next-Generation Sequencing Assay for Carrier Screening in Old Order Amish and Mennonite Populations of Pennsylvania Published: July 1, 2019 Publication: The Journal of Molecular Diagnostics

Authors: Erin L. Crowgey, Michael C. Washburn, E. Anders Kolb, Erik G. Puffenberger

Abstract:
Genetically isolated populations, such as the Old Order Amish and Old Order Mennonite communities, have an increased incidence of specific autosomal recessive disorders caused by the founder effect. In these populations, robust expanded carrier screening and diagnostic testing have the potential to reduce overall medical costs and improve patient outcomes. A novel next-generation sequencing assay was developed using anchored multiplex PCR technology (ArcherDX) for 162 different genetic syndromes caused by 202 pathogenic variants consisting of 150 single-nucleotide changes, 43 small insertion/deletions, and 9 large deletions (>20 nucleotides). To assess the accuracy of the screening panel results, 48 samples were selected on the basis of prior whole exome sequencing results. An additional 15 samples were chosen specifically to validate SMN1 and SMN2 copy number analyses. Collectively, the screening panel detected 273 pathogenic single-nucleotide or small insertion/deletion variants, 35 copy number variations, and 1 chromosomal abnormality (Klinefelter syndrome). Concordance with prior whole exome sequencing was 100%. By using a novel next-generation sequencing workflow, a successful targeted gene variant panel was developed for the Old Order Amish and Old Order Mennonite populations of Lancaster County, Pennsylvania. Population-wide carrier screening may help decrease the morbidity and mortality of these conditions in the high-risk populations.
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Title: Heritability of complex white matter diffusion traits assessed in a population isolate Published: February 1, 2016 Publication: Human Brain Mapping

Authors: Kochunov P, Fu M, Nugent K, Wright SN, Du X, Muellerklein F, Morrissey M, Eskandar G, Shukla DK, Jahanshad N, Thompson PM, Patel B, Postolache TT, Strauss KA, Shuldiner AR, Mitchell BD, Hong LE

Abstract:
Diffusion weighted imaging (DWI) methods can noninvasively ascertain cerebral microstructure by examining pattern and directions of water diffusion in the brain. We calculated heritability for DWI parameters in cerebral white (WM) and gray matter (GM) to study the genetic contribution to the diffusion signals across tissue boundaries.
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Title: Development of DNA Confirmatory and High-Risk Diagnostic Testing for Newborns Using Targeted Next-Generation DNA Sequencing Published: May 1, 2015 Publication: Genetics in Medicine

Authors: Bhattacharjee, A, Sokolsky, T, Wyman, SK, Reese, MG, Puffenberger, EG, Strauss, KA, Morton, DH, Parad, RB, Naylor, EW

Abstract:
Genetic testing is routinely used for second-tier confirmation of newborn sequencing results to rule out false positives and to confirm diagnoses in newborns undergoing inpatient and outpatient care. We developed a targeted next-generation sequencing panel coupled with a variant processing pipeline and demonstrated utility and performance benchmarks across multiple newborn disease presentations in a retrospective clinical study.
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Title: One Community’s Effort to Control Genetic Disease Published: May 17, 2012 Publication: American Journal of Public Health

Authors: Strauss KA, Puffenberger EG, Morton DH

Abstract:
In 1989, we established a small community health clinic to provide care for uninsured Amish and Mennonite children with genetic disorders. Over 20 years, we have used publicly available molecular data and sophisticated technologies to improve diagnostic efficiency, control laboratory costs, reduce hospitalizations, and prevent major neurological impairments within a rural underserved community. These actions allowed the clinic’s 2010 operating budget of $1.5 million to save local communities an estimated $20 to $25 million in aggregate medical costs. This exposes an unsettling fact: our failure to improve the lot of most people stricken with genetic disease is no longer a matter of scientific ignorance or prohibitive costs but of choices we make about how to implement existing knowledge and resources.
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Title: Genetic mapping and exome sequencing identify variants associated with five novel diseases Published: January 17, 2012 Publication: PLOS One

Authors: Puffenberger EG, Jinks RN, Sougnez C, Cibulskis K, Willert RA, Achilly NP, Cassidy RP, Fiorentini CJ, Heiken KF, Lawrence JJ, Mahoney MH, Miller CJ, Nair DT, Politi KA, Worcester KN, Setton RA, Dipiazza R, Sherman EA, Eastman JT, Francklyn C, Robey-Bond S, Rider NL, Gabriel S, Morton DH, Strauss KA

Abstract:
The Clinic for Special Children (CSC) has integrated biochemical and molecular methods into a rural pediatric practice serving Old Order Amish and Mennonite (Plain) children. Among the Plain people, we have used single nucleotide polymorphism (SNP) microarrays to genetically map recessive disorders to large autozygous haplotype blocks (mean = 4.4 Mb) that contain many genes (mean = 79). For some, uninformative mapping or large gene lists preclude disease-gene identification by Sanger sequencing. Seven such conditions were selected for exome sequencing at the Broad Institute; all had been previously mapped at the CSC using low density SNP microarrays coupled with autozygosity and linkage analyses. Using between 1 and 5 patient samples per disorder, we identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. Our results reveal the power of coupling new genotyping technologies to population-specific genetic knowledge and robust clinical data.
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Title: A founder mutation in BBS2 is responsible for Bardet-Biedl syndrome in the Hutterite population: utility of SNP arrays in genetically heterogeneous disorders Published: November 1, 2010 Publication: Clinical Genetics

Authors: Innes AM, Boycott KM, Puffenberger EG, Redl D, MacDonald IM, Chudley AE, Beaulieu C, Perrier R, Gillan T, Wade A, Parboosingh JS

Abstract:
Bardet-Biedl syndrome (BBS) is a multisystem genetically heterogeneous disorder, the clinical features of which are largely the consequence of ciliary dysfunction. BBS is typically inherited in an autosomal recessive fashion, and mutations in at least 14 genes have been identified. Here, we report the identification of a founder mutation in the BBS2 gene as the cause for the increased incidence of this developmental disorder in the Hutterite population. To ascertain the Hutterite BBS locus, we performed a genome-wide single nucleotide polymorphism (SNP) analysis on a single patient and his three unaffected siblings from a Hutterite family. The analysis identified two large SNP blocks that were homozygous in the patient but not in his unaffected siblings, one of these regions contained the BBS2 gene. Sequence analysis and subsequent RNA studies identified and confirmed a novel splice site mutation, c.472-2A>G, in BBS2. This mutation was also found in homozygous form in three subsequently studied Hutterite BBS patients from two different leuts, confirming that this is a founder mutation in the Hutterite population. Further studies are required to determine the frequency of this mutation and its role, if any, in the expression of other ciliopathies in this population.
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Title: Genetics, medicine, and the Plain people Published: July 16, 2009 Publication: Annual Review of Genomics and Human Genetics

Authors: Strauss KA, Puffenberger EG

Abstract:
The Old Order Amish and Old Order Mennonite populations of Pennsylvania are descended from Swiss Anabaptist immigrants who came to the New World in the early eighteenth century. Today they live in many small endogamous demes across North America. Genetically, these demes have dissimilar allele frequencies and disease spectra owing to unique founders. Biological and social aspects of Old Order communities make them ideal for studies in population genetics and genomic medicine, and over the last 40 years, advances in genomic science coincided with investigational studies in Plain populations. Newer molecular genetic technologies are sufficiently informative, rapid, and flexible to use in a clinical setting, and we have successfully integrated these tools into a rural pediatric practice. Our studies with the Pennsylvania Plain communities show that population-specific genetic knowledge provides a powerful framework in which to prevent disease, reduce medical costs, and create new insights into human biology.
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Title: A multiplex human syndrome implicates a key role for intestinal cell kinase in development of central nervous, skeletal, and endocrine systems Published: February 13, 2009 Publication: The American Journal of Human Genetics

Authors: Lahiry P, Wang J, Robinson JF, Turowec JP, Litchfield DW, Lanktree MB, Gloor GB, Puffenberger EG, Strauss KA, Martens MB, Ramsay DA, Rupar CA, Siu V, Hegele RA

Abstract:
Six infants in an Old Order Amish pedigree were observed to be affected with endocrine-cerebro-osteodysplasia (ECO). ECO is a previously unidentified neonatal lethal recessive disorder with multiple anomalies involving the endocrine, cerebral, and skeletal systems. Autozygosity mapping and sequencing identified a previously unknown missense mutation, R272Q, in ICK, encoding intestinal cell kinase (ICK). Our results established that R272 is conserved across species and among ethnicities, and three-dimensional analysis of the protein structure suggests protein instability due to the R272Q mutation. We also demonstrate that the R272Q mutant fails to localize at the nucleus and has diminished kinase activity. These findings suggest that ICK plays a key role in the development of multiple organ systems.
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Title: Clinical application of DNA microarrays: molecular diagnosis and HLA matching of an Amish child with severe combined immune deficiency Published: July 1, 2008 Publication: Clinical Immunology

Authors: Strauss KA, Puffenberger EG, Bunin N, Rider NL, Morton MC, Eastman JT 3rd, Morton DH

Abstract:
Amish and Mennonite children with severe combined immune deficiency (SCID) often die without treatment as a result of delayed diagnoses and prohibitive costs of therapy. In this detailed case report, we describe the novel use of DNA microarrays to improve the diagnosis and management of an Amish infant with SCID. Using 10,000 single nucleotide polymorphism (SNP) genotypes from the patient, her parents, and seven siblings, we identified the recombinase activating genes for diagnostic sequencing, and then characterized a novel pathogenic variant in RAG1 (c.2974A>G). The same genotype data were used to identify a sibling stem cell donor who was haplo-identical at human leukocyte antigen (HLA) and blood group (ABO) loci. Autozygosity and linkage analysis of SNP genotypes within a family narrows the search for SCID candidate genes and provides a relatively simple and inexpensive way to identify potential tissue donors among biological siblings.
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Title: Second-tier test for quantification of alloisoleucine and branched-chain amino acids in dried blood spots to improve newborn screening for maple syrup urine disease (MSUD) Published: March 1, 2008 Publication: Clinical Chemistry

Authors: Oglesbee D, Sanders KA, Lacey JM, Magera MJ, Casetta B, Strauss KA, Tortorelli S, Rinaldo P, Matern D

Abstract:
Newborn screening for maple syrup urine disease (MSUD) relies on finding increased concentrations of the branched-chain amino acids (BCAAs) leucine, isoleucine, and valine by tandem mass spectrometry (MS/MS). d-Alloisoleucine (allo-Ile) is the only pathognomonic marker of MSUD, but it cannot be identified by existing screening methods because it is not differentiated from isobaric amino acids. Furthermore, newborns receiving total parenteral nutrition often have increased concentrations of BCAAs. To improve the specificity of newborn screening for MSUD and to reduce the number of diet-related false-positive results, we developed a LC-MS/MS method for quantifying allo-Ile.
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Title: Genome-wide SNP arrays as a diagnostic tool: clinical description, genetic mapping, and molecular characterization of Salla disease in an Old Order Mennonite population Published: October 15, 2005 Publication: American Journal of Medical Genetics Part A

Authors: Strauss KA, Puffenberger EG, Craig DW, Panganiban CB, Lee AM, Hu-Lince D, Stephan DA, Morton DH

Abstract:
An Old Order Mennonite child was evaluated for gross motor delay, truncal ataxia, and slow linear growth. The diagnostic evaluation, which included sub-specialty consultations, neuroimaging, and metabolic testing, was long, costly, and did not yield a diagnosis. Recognition of a similarly affected second cousin prompted a genome-wide homozygosity mapping study using high-density single nucleotide polymorphism (SNP) arrays. SNP genotypes from two affected individuals and their parents were used to localize the disease locus to a 14.9 Mb region on chromosome 6. This region contained 55 genes, including SLC17A5, the gene encoding the lysosomal N-acetylneuraminic acid transport protein. Direct sequencing of SLC17A5 in the proband revealed homozygosity for the 115C --> T (R39C) sequence variant, the common cause of Salla disease in Finland. Three additional affected Mennonite individuals, ages 8 months to 50 years, were subsequently identified by directed molecular genetic testing. This small-scale mapping study was rapid, inexpensive, and analytically simple. In families with shared genetic heritage, genome-wide SNP arrays with relatively high marker density allow disease gene mapping studies to be incorporated into routine diagnostic evaluations.
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Title: Identification of disease causing loci using an array-based genotyping approach on pooled DNA Published: September 30, 2005 Publication: BMC Genomics

Authors: Craig DW, Huentelman MJ, Hu-Lince D, Zismann VL, Kruer MC, Lee AM, Puffenberger EG, Pearson JM, Stephan DA

Abstract:
Pooling genomic DNA samples within clinical classes of disease followed by genotyping on whole-genome SNP microarrays, allows for rapid and inexpensive genome-wide association studies. Key to the success of these studies is the accuracy of the allelic frequency calculations, the ability to identify false-positives arising from assay variability and the ability to better resolve association signals through analysis of neighbouring SNPs.
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Title: Diagnosis and management of glutaric aciduria type I Published: June 1, 1998 Publication: Journal of Inherited Metabolic Disease

Authors: Baric I, Zschocke J, Christensen E, Duran M, Goodman SI, Leonard JV, Müller E, Morton DH, Superti-Furga A, Hoffmann GF

Abstract:
Glutaric aciduria type I (GA1) is a preventable cause of acute brain damage in early childhood, leading to a severe dystonic-dyskinetic disorder that is similar to cerebral palsy and ranges from extreme hypotonia to choreoathetosis to rigidity with spasticity. Degeneration of the putamen and caudate typically occurs between 6 and 18 months of age and is probably linked to changes in metabolic demand caused by normal maturational changes and superimposed catabolic stress. Recognition of this biochemical disorder before the brain has been injured is essential to outcome. Diagnosis depends upon the recognition of relatively non-specific physical findings such as hypotonia, irritability and macrocephaly, and on performance of urine organic acid quantification by gas chromatography--mass spectrometry or selective searches of urine or blood specimens by tandem mass spectrometry for glutarylcarnitine. The diagnosis may also be suggested by characteristic findings on neuroimaging. In selected patients diagnosis can only be reached by enzyme assay. Specific current management by the authors of this paper includes pharmacological doses of L-carnitine, as well as dietary protein restriction. Metabolic decompensation must be treated aggressively to avoid permanent brain damage. Multicentre studies are needed to establish best methods of diagnosis and optimal therapy of this disorder.
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Title: 3-Methylcrotonyl-coenzyme A carboxylase deficiency in Amish/Mennonite adults identified by detection of increased acylcarnitines in blood spots of their children Published: March 1, 1998 Publication: The Journal of Pediatrics

Authors: Gibson KM, Bennett MJ, Naylor EW, Morton DH

Abstract:
Isolated 3-methylcrotonyl coenzyme A carboxylase (MCC) deficiency was documented in four adult women from the Amish/Mennonite population of Lancaster County, Pennsylvania. Metabolic and enzymatic investigations in these individuals were instituted after the detection of abnormal acylcarnitine profiles in blood spots obtained from their newborn children, in whom MCC activity was normal.
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Title: Brain magnetic resonance imaging in suspected extrapyramidal cerebral palsy: observations in distinguishing genetic-metabolic from acquired causes Published: August 1, 1997 Publication: The Journal of Pediatrics

Authors: Hoon AH Jr, Reinhardt EM, Kelley RI, Breiter SN, Morton DH, Naidu SB, Johnston MV

Abstract:
Experienced clinicians recognize that some children who appear to have static cerebral palsy (CP) actually have underlying genetic-metabolic disorders. We report a series of patients with motor disorders seen in children with extrapyramidal CP in whom brain magnetic resonance imaging abnormalities provided important diagnostic clues in distinguishing genetic-metabolic disorders from other causes. One cause of static extrapyramidal CP, hypoxic-ischemic encephalopathy at the end of a term gestation, produces a characteristic pattern of hyperintense signal and atrophy in the putamen and thalamus. Other signal abnormalities and atrophy in the putamen, globus pallidus, or caudate can point to genetic-metabolic diseases, including disorders of mitochondrial and organic acid metabolism. Progress in understanding and treating genetic diseases of the developing brain makes it essential to diagnose disorders that masquerade as static CP. Brain magnetic resonance imaging is a useful diagnostic tool in the initial evaluation of children who appear to have CP.
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