101
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Rovozzo R, Korza G, Baker MW, Li M, Bhattacharyya A, Barbarese E, Carson JH. CGG Repeats in the 5'UTR of FMR1 RNA Regulate Translation of Other RNAs Localized in the Same RNA Granules. PLoS One 2016; 11:e0168204. [PMID: 28005950 PMCID: PMC5179066 DOI: 10.1371/journal.pone.0168204] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/28/2016] [Indexed: 01/24/2023] Open
Abstract
CGG repeats in the 5’UTR of Fragile X Mental Retardation 1 (FMR1) RNA mediate RNA localization and translation in granules. Large expansions of CGG repeats (> 200 repeats) in FMR1, referred to as full mutations, are associated with fragile X syndrome (FXS). Smaller expansions (55–200 repeats), referred to as premutations, are associated with fragile X tremor ataxia syndrome (FXTAS) and fragile X premature ovarian insufficiency (FXPOI). TMPyP4 is a porphyrin ring compound that destabilizes CGG repeat RNA secondary structure. Here we show that exogenous CGG repeat RNA by itself, lacking the FMRP ORF, microinjected into hippocampal neurons is localized in RNA granules and inhibits translation of ARC RNA, which is localized in the same granules. TMPyP4 rescues translation of ARC RNA in granules. We also show that in human premutation fibroblasts with endogenous CGG repeat expansions in the FMR1 gene, translation of ARC RNA is inhibited and calcium homeostasis is disrupted and both phenotypes are rescued by TMPyP4. Inhibition of granule translation by expanded CGG repeats and rescue of granule translation by TMPy4, represent potential pathogenic mechanism and therapeutic strategy, respectively, for FXTAS and FXPOI.
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Affiliation(s)
- René Rovozzo
- Center for Cell Analysis and Modeling, UConn Health, Farmington, Connecticut, United States of America
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, United States of America
| | - Mei W. Baker
- Departments of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin State Laboratory of Hygiene, Newborn Screening Laboratory, Madison, Wisconsin, United States of America
| | - Meng Li
- Waisman Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Anita Bhattacharyya
- Waisman Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Elisa Barbarese
- Department of Neuroscience, UConn Health, Farmington, Connecticut, United States of America
| | - John H. Carson
- Center for Cell Analysis and Modeling, UConn Health, Farmington, Connecticut, United States of America
- * E-mail:
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102
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Macpherson JN, Murray A. Development of Genetic Testing for Fragile X Syndrome and Associated Disorders, and Estimates of the Prevalence of FMR1 Expansion Mutations. Genes (Basel) 2016; 7:genes7120110. [PMID: 27916885 PMCID: PMC5192486 DOI: 10.3390/genes7120110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/10/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022] Open
Abstract
The identification of a trinucleotide (CGG) expansion as the chief mechanism of mutation in Fragile X syndrome in 1991 heralded a new chapter in molecular diagnostic genetics and generated a new perspective on mutational mechanisms in human genetic disease, which rapidly became a central paradigm (“dynamic mutation”) as more and more of the common hereditary neurodevelopmental disorders were ascribed to this novel class of mutation. The progressive expansion of a CGG repeat in the FMR1 gene from “premutation” to “full mutation” provided an explanation for the “Sherman paradox,” just as similar expansion mechanisms in other genes explained the phenomenon of “anticipation” in their pathogenesis. Later, FMR1 premutations were unexpectedly found associated with two other distinct phenotypes: primary ovarian insufficiency and tremor-ataxia syndrome. This review will provide a historical perspective on procedures for testing and reporting of Fragile X syndrome and associated disorders, and the population genetics of FMR1 expansions, including estimates of prevalence and the influence of AGG interspersions on the rate and probability of expansion.
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Affiliation(s)
- James N Macpherson
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury SP2 8BJ, UK.
| | - Anna Murray
- Medical School, University of Exeter, RILD Level 3, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK.
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103
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De Bustos A, Cuadrado A, Jouve N. Sequencing of long stretches of repetitive DNA. Sci Rep 2016; 6:36665. [PMID: 27819354 PMCID: PMC5098217 DOI: 10.1038/srep36665] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/18/2016] [Indexed: 01/13/2023] Open
Abstract
Repetitive DNA is widespread in eukaryotic genomes, in some cases making up more than 80% of the total. SSRs are a type of repetitive DNA formed by short motifs repeated in tandem arrays. In some species, SSRs may be organized into long stretches, usually associated with the constitutive heterochromatin. Variation in repeats can alter the expression of genes, and changes in the number of repeats have been linked to certain human diseases. Unfortunately, the molecular characterization of these repeats has been hampered by technical limitations related to cloning and sequencing. Indeed, most sequenced genomes contain gaps owing to repetitive DNA-related assembly difficulties. This paper reports an alternative method for sequencing of long stretches of repetitive DNA based on the combined use of 1) a linear vector to stabilize the cloning process, and 2) the use of exonuclease III for obtaining progressive deletions of SSR-rich fragments. This strategy allowed the sequencing of a fragment containing a stretch of 6.2 kb of continuous SSRs. To demonstrate that this procedure can sequence other kinds of repetitive DNA, it was used to examine a 4.5 kb fragment containing a cluster of 15 repeats of the 5S rRNA gene of barley.
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Affiliation(s)
- Alfredo De Bustos
- Department of Biomedicine and Biotechnology, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Angeles Cuadrado
- Department of Biomedicine and Biotechnology, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
| | - Nicolás Jouve
- Department of Biomedicine and Biotechnology, University of Alcala, 28871 Alcalá de Henares (Madrid), Spain
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104
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Kaseniit KE, Theilmann MR, Robertson A, Evans EA, Haque IS. Group Testing Approach for Trinucleotide Repeat Expansion Disorder Screening. Clin Chem 2016; 62:1401-8. [DOI: 10.1373/clinchem.2016.259796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/22/2016] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Fragile X syndrome (FXS, OMIM #300624) is an X-linked condition caused by trinucleotide repeat expansions in the 5′ UTR (untranslated region) of the fragile X mental retardation 1 (FMR1) gene. FXS testing is commonly performed in expanded carrier screening and has been proposed for inclusion in newborn screening. However, because pathogenic alleles are long and have low complexity (>200 CGG repeats), FXS is currently tested by a single-plex electrophoresis-resolved PCR assay rather than multiplexed approaches like next-generation sequencing or mass spectrometry. In this work, we sought an experimental design based on nonadaptive group testing that could accurately and reliably identify the size of abnormally expanded FMR1 alleles of males and females.
METHODS
We developed a new group testing scheme named StairCase (SC) that was designed to the constraints of the FXS testing problem, and compared its performance to existing group testing schemes by simulation. We experimentally evaluated SC's performance on 210 samples from the Coriell Institute biorepositories using pooled PCR followed by capillary electrophoresis on 3 replicates of each of 3 pooling layouts differing by the mapping of samples to pools.
RESULTS
The SC pooled PCR approach demonstrated perfect classification of samples by clinical category (normal, intermediate, premutation, or full mutation) for 90 positives and 1800 negatives, with a batch of 210 samples requiring only 21 assays.
CONCLUSIONS
Group testing based on SC is an implementable approach to trinucleotide repeat expansion disorder testing that offers ≥10-fold reduction in assay costs over current single-plex methods.
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105
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Khodakov D, Wang C, Zhang DY. Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches. Adv Drug Deliv Rev 2016; 105:3-19. [PMID: 27089811 DOI: 10.1016/j.addr.2016.04.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/21/2016] [Accepted: 04/06/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics.
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106
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Affiliation(s)
- Shawn E. Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806; ,
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806; ,
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107
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Ishiura H, Tsuji S. Epidemiology and molecular mechanism of frontotemporal lobar degeneration/amyotrophic lateral sclerosis with repeat expansion mutation in C9orf72. J Neurogenet 2016; 29:85-94. [PMID: 26540641 DOI: 10.3109/01677063.2015.1085980] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
GGGGCC hexanucleotide repeat expansions in C9orf72 were identified in 2011 as the genetic cause of frontotemporal lobar degeneration (FTLD)/amyotrophic lateral sclerosis (ALS) linked to chromosome 9. Since then, a number of studies have been conducted to delineate the molecular epidemiology of the repeat expansions and the molecular pathophysiology of the disease. The frequency of the repeat expansions considerably varied among countries. The frequency of the repeat expansions was high in European populations and populations of European descent and a substantial proportion of sporadic FTLD or ALS patients also have the mutations in these populations. On the other hand, the frequency was extremely low in Asia or Oceania except for limited regions including Kii Peninsula of Japan. A founder effect seems to strongly influence the regional differences in the frequency, but there is no definitive evidence that supports the notion that the repeat expansions arose in a single founder or multiple founders. As a disease-causing mechanism, several molecular mechanisms have been proposed, including conformational changes of DNA (G-quadruplex formation and hypermethylation) or RNA (G-quadruplex formation) molecules, altered transcriptional levels of C9orf72, sequestration of RNA-binding proteins, bidirectional transcription, formation of RNA foci, and neurotoxicity of dipeptide repeat proteins generated by repeat-associated non-ATG-initiated translation. Further investigations on the molecular mechanisms of neurodegeneration are expected to lead to the development of therapeutic interventions for this disease as well as for other diseases associated with non-coding repeat expansions.
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Affiliation(s)
- Hiroyuki Ishiura
- a Department of Neurology , The University of Tokyo , Tokyo , Japan
| | - Shoji Tsuji
- a Department of Neurology , The University of Tokyo , Tokyo , Japan
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108
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Liljegren MM, de Muinck EJ, Trosvik P. Microsatellite Length Scoring by Single Molecule Real Time Sequencing - Effects of Sequence Structure and PCR Regime. PLoS One 2016; 11:e0159232. [PMID: 27414800 PMCID: PMC4945053 DOI: 10.1371/journal.pone.0159232] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/29/2016] [Indexed: 12/02/2022] Open
Abstract
Microsatellites are DNA sequences consisting of repeated, short (1–6 bp) sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT) sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level.
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Affiliation(s)
- Mikkel Meyn Liljegren
- Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway
| | - Eric Jacques de Muinck
- Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway
| | - Pål Trosvik
- Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway
- * E-mail:
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109
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Suzuki Y, Korlach J, Turner SW, Tsukahara T, Taniguchi J, Qu W, Ichikawa K, Yoshimura J, Yurino H, Takahashi Y, Mitsui J, Ishiura H, Tsuji S, Takeda H, Morishita S. AgIn: measuring the landscape of CpG methylation of individual repetitive elements. Bioinformatics 2016; 32:2911-9. [PMID: 27318202 PMCID: PMC5039925 DOI: 10.1093/bioinformatics/btw360] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/03/2016] [Indexed: 12/18/2022] Open
Abstract
Motivation: Determining the methylation state of regions with high copy numbers is challenging for second-generation sequencing, because the read length is insufficient to map reads uniquely, especially when repetitive regions are long and nearly identical to each other. Single-molecule real-time (SMRT) sequencing is a promising method for observing such regions, because it is not vulnerable to GC bias, it produces long read lengths, and its kinetic information is sensitive to DNA modifications. Results: We propose a novel linear-time algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Using a practical read coverage of ∼30-fold from an inbred strain medaka (Oryzias latipes), we observed that both the sensitivity and precision of our method on individual CpG sites were ∼93.7%. We also observed a high correlation coefficient (R = 0.884) between our method and bisulfite sequencing, and for 92.0% of CpG sites, methylation levels ranging over [0,1] were in concordance within an acceptable difference 0.25. Using this method, we characterized the landscape of the methylation status of repetitive elements, such as LINEs, in the human genome, thereby revealing the strong correlation between CpG density and hypomethylation and detecting hypomethylation hot spots of LTRs and LINEs. We uncovered the methylation states for nearly identical active transposons, two novel LINE insertions of identity ∼99% and length 6050 base pairs (bp) in the human genome, and 16 Tol2 elements of identity >99.8% and length 4682 bp in the medaka genome. Availability and Implementation: AgIn (Aggregate on Intervals) is available at: https://github.com/hacone/AgIn Contact:ysuzuki@cb.k.u-tokyo.ac.jp or moris@cb.k.u-tokyo.ac.jp Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuta Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | | | | | - Tatsuya Tsukahara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junko Taniguchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Wei Qu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Hideaki Yurino
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Yuji Takahashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
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110
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Pham TT, Yin J, Eid JS, Adams E, Lam R, Turner SW, Loomis EW, Wang JY, Hagerman PJ, Hanes JW. Single-locus enrichment without amplification for sequencing and direct detection of epigenetic modifications. Mol Genet Genomics 2016; 291:1491-504. [PMID: 26825750 DOI: 10.1007/s00438-016-1167-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 01/06/2016] [Indexed: 12/16/2022]
Abstract
A gene-level targeted enrichment method for direct detection of epigenetic modifications is described. The approach is demonstrated on the CGG-repeat region of the FMR1 gene, for which large repeat expansions, hitherto refractory to sequencing, are known to cause fragile X syndrome. In addition to achieving a single-locus enrichment of nearly 700,000-fold, the elimination of all amplification steps removes PCR-induced bias in the repeat count and preserves the native epigenetic modifications of the DNA. In conjunction with the single-molecule real-time sequencing approach, this enrichment method enables direct readout of the methylation status and the CGG repeat number of the FMR1 allele(s) for a clonally derived cell line. The current method avoids potential biases introduced through chemical modification and/or amplification methods for indirect detection of CpG methylation events.
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Affiliation(s)
| | - Jun Yin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, CA, 95616, USA.,Dendrite Morphogenesis and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
| | - John S Eid
- Pacific Biosciences, Menlo Park, CA, 94025, USA.,Whole Biome, Inc., San Francisco, CA, 94107, USA
| | - Evan Adams
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, CA, 95616, USA
| | - Regina Lam
- Pacific Biosciences, Menlo Park, CA, 94025, USA
| | | | - Erick W Loomis
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, CA, 95616, USA.,Faculty of Medicine, Department of Surgery & Cancer, Institute of Reproductive and Developmental Biology, Hammersmith Campus Imperial College London, London, UK
| | - Jun Yi Wang
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, CA, 95616, USA
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Davis, CA, 95616, USA
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111
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Engineered Nucleases and Trinucleotide Repeat Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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112
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Lee SS, Bohrson C, Pike AM, Wheelan SJ, Greider CW. ATM Kinase Is Required for Telomere Elongation in Mouse and Human Cells. Cell Rep 2015; 13:1623-32. [PMID: 26586427 PMCID: PMC4663052 DOI: 10.1016/j.celrep.2015.10.035] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 09/11/2015] [Accepted: 10/11/2015] [Indexed: 12/26/2022] Open
Abstract
Short telomeres induce a DNA damage response, senescence, and apoptosis, thus maintaining telomere length equilibrium is essential for cell viability. Telomerase addition of telomere repeats is tightly regulated in cells. To probe pathways that regulate telomere addition, we developed the ADDIT assay to measure new telomere addition at a single telomere in vivo. Sequence analysis showed telomerase-specific addition of repeats onto a new telomere occurred in just 48 hr. Using the ADDIT assay, we found that ATM is required for addition of new repeats onto telomeres in mouse cells. Evaluation of bulk telomeres, in both human and mouse cells, showed that blocking ATM inhibited telomere elongation. Finally, the activation of ATM through the inhibition of PARP1 resulted in increased telomere elongation, supporting the central role of the ATM pathway in regulating telomere addition. Understanding this role of ATM may yield new areas for possible therapeutic intervention in telomere-mediated disease.
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Affiliation(s)
- Stella Suyong Lee
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Predoctoral Training Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Craig Bohrson
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexandra Mims Pike
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sarah Jo Wheelan
- Predoctoral Training Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Carol Widney Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Predoctoral Training Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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113
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Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives. BIOMED RESEARCH INTERNATIONAL 2015; 2015:161648. [PMID: 26665001 PMCID: PMC4668301 DOI: 10.1155/2015/161648] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 09/30/2015] [Accepted: 10/18/2015] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) technologies have greatly impacted on every field of molecular research mainly because they reduce costs and increase throughput of DNA sequencing. These features, together with the technology's flexibility, have opened the way to a variety of applications including the study of the molecular basis of human diseases. Several analytical approaches have been developed to selectively enrich regions of interest from the whole genome in order to identify germinal and/or somatic sequence variants and to study DNA methylation. These approaches are now widely used in research, and they are already being used in routine molecular diagnostics. However, some issues are still controversial, namely, standardization of methods, data analysis and storage, and ethical aspects. Besides providing an overview of the NGS-based approaches most frequently used to study the molecular basis of human diseases at DNA level, we discuss the principal challenges and applications of NGS in the field of human genomics.
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114
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Rhoads A, Au KF. PacBio Sequencing and Its Applications. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:278-89. [PMID: 26542840 PMCID: PMC4678779 DOI: 10.1016/j.gpb.2015.08.002] [Citation(s) in RCA: 1171] [Impact Index Per Article: 130.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/06/2015] [Accepted: 08/11/2015] [Indexed: 12/15/2022]
Abstract
Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing (SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with diseases. Moreover, PacBio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes, due to its ability to sequence full-length transcripts or fragments with significant lengths. Additionally, PacBio’s sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using PacBio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with PacBio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. The advent of PacBio sequencing has made available much information that could not be obtained via SGS alone.
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Affiliation(s)
- Anthony Rhoads
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Kin Fai Au
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA.
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115
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Abstract
Fragile X syndrome (FXS), a trinucleotide repeat disorder, is the most common heritable form of cognitive impairment. Since the discovery of the FMR1 gene in 1991, great strides have been made in the field of molecular diagnosis for FXS. Cytogenetic analysis, which was the method of diagnosis in the early 1990, was replaced by Southern blot and PCR analysis albeit with some limitations. In the past few years many PCR-based methodologies, able to amplify large full mutation expanded alleles, with or without methylation, have been proposed. Reviewed here are the advantages, disadvantages and limitations of the most recent developments in the field of FXS diagnosis.
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Affiliation(s)
- Flora Tassone
- a Department of Biochemistry and Molecular Medicine , University of California, Davis, School of Medicine , Davis , CA 95616 , USA.,b MIND Institute , University of California Davis Medical Center , Sacramento , CA 95817 , USA
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116
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McFarland KN, Liu J, Landrian I, Godiska R, Shanker S, Yu F, Farmerie WG, Ashizawa T. SMRT Sequencing of Long Tandem Nucleotide Repeats in SCA10 Reveals Unique Insight of Repeat Expansion Structure. PLoS One 2015; 10:e0135906. [PMID: 26295943 PMCID: PMC4546671 DOI: 10.1371/journal.pone.0135906] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 07/28/2015] [Indexed: 12/02/2022] Open
Abstract
A large, non-coding ATTCT repeat expansion causes the neurodegenerative disorder, spinocerebellar ataxia type 10 (SCA10). In a subset of SCA10 patients, interruption motifs are present at the 5’ end of the expansion and strongly correlate with epileptic seizures. Thus, interruption motifs are a predictor of the epileptic phenotype and are hypothesized to act as a phenotypic modifier in SCA10. Yet, the exact internal sequence structure of SCA10 expansions remains unknown due to limitations in current technologies for sequencing across long extended tracts of tandem nucleotide repeats. We used the third generation sequencing technology, Single Molecule Real Time (SMRT) sequencing, to obtain full-length contiguous expansion sequences, ranging from 2.5 to 4.4 kb in length, from three SCA10 patients with different clinical presentations. We obtained sequence spanning the entire length of the expansion and identified the structure of known and novel interruption motifs within the SCA10 expansion. The exact interruption patterns in expanded SCA10 alleles will allow us to further investigate the potential contributions of these interrupting sequences to the pathogenic modification leading to the epilepsy phenotype in SCA10. Our results also demonstrate that SMRT sequencing is useful for deciphering long tandem repeats that pose as “gaps” in the human genome sequence.
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Affiliation(s)
- Karen N. McFarland
- Department of Neurology and The McKnight Brain Institute, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Jilin Liu
- Department of Neurology and The McKnight Brain Institute, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Ivette Landrian
- Department of Neurology and The McKnight Brain Institute, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Ronald Godiska
- Lucigen Corporation, Middleton, Wisconsin, 53562, United States of America
| | - Savita Shanker
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Fahong Yu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, United States of America
| | - William G. Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology and The McKnight Brain Institute, University of Florida, Gainesville, Florida, 32610, United States of America
- * E-mail:
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Lyons JI, Kerr GR, Mueller PW. Fragile X Syndrome: Scientific Background and Screening Technologies. J Mol Diagn 2015; 17:463-71. [PMID: 26162330 DOI: 10.1016/j.jmoldx.2015.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 03/05/2015] [Accepted: 04/02/2015] [Indexed: 11/26/2022] Open
Abstract
Fragile X is the most common inherited cause of mental retardation with a prevalence of 1 in 4000 for males and 1 in 5000 to 8000 for females. The American College of Medical Genetics and Genomics has recommended diagnostic testing for fragile X in symptomatic persons, women with ovarian dysfunction, and persons with tremor/ataxia syndrome. Although medical and scientific professionals do not currently recommend screening nonsymptomatic populations, improvements in current treatment approaches and ongoing clinical trials have generated growing interest in screening for fragile X. Here, we briefly review the relevant molecular basis of fragile X and fragile X testing and compare three different molecular technologies available for fragile X screening in both males and females. These technologic approaches include destabilizing the CGG-repeat region with betaine and using chimeric CGG-targeted PCR primers, using heat pulses to destabilize C-G bonds in the PCR extension step, and using melting curve analysis to differentiate expanded CGG repeats from normals. The first two-step method performed with high sensitivity and specificity. The second method provided agarose gel images that allow identification of males with expanded CGG repeats and females with expanded CGG-repeat bands which are sometimes faint. The third melting curve analysis method would require controls in each run to correct for shifting optimal cutoff values.
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Affiliation(s)
- Justine I Lyons
- Molecular Risk Assessment Laboratory, Newborn Screening and Molecular Biology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Gregory R Kerr
- Molecular Risk Assessment Laboratory, Newborn Screening and Molecular Biology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Patricia W Mueller
- Molecular Risk Assessment Laboratory, Newborn Screening and Molecular Biology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia.
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Abstract
The human genome sequence has profoundly altered our understanding of biology, human diversity, and disease. The path from the first draft sequence to our nascent era of personal genomes and genomic medicine has been made possible only because of the extraordinary advancements in DNA sequencing technologies over the past 10 years. Here, we discuss commonly used high-throughput sequencing platforms, the growing array of sequencing assays developed around them, as well as the challenges facing current sequencing platforms and their clinical application.
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Affiliation(s)
- Jason A Reuter
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Damek V Spacek
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Wang M, Beck CR, English AC, Meng Q, Buhay C, Han Y, Doddapaneni HV, Yu F, Boerwinkle E, Lupski JR, Muzny DM, Gibbs RA. PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics 2015; 16:214. [PMID: 25887218 PMCID: PMC4376517 DOI: 10.1186/s12864-015-1370-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/20/2015] [Indexed: 11/24/2022] Open
Abstract
Background Generation of long (>5 Kb) DNA sequencing reads provides an approach for interrogation of complex regions in the human genome. Currently, large-insert whole genome sequencing (WGS) technologies from Pacific Biosciences (PacBio) enable analysis of chromosomal structural variations (SVs), but the cost to achieve the required sequence coverage across the entire human genome is high. Results We developed a method (termed PacBio-LITS) that combines oligonucleotide-based DNA target-capture enrichment technologies with PacBio large-insert library preparation to facilitate SV studies at specific chromosomal regions. PacBio-LITS provides deep sequence coverage at the specified sites at substantially reduced cost compared with PacBio WGS. The efficacy of PacBio-LITS is illustrated by delineating the breakpoint junctions of low copy repeat (LCR)-associated complex structural rearrangements on chr17p11.2 in patients diagnosed with Potocki–Lupski syndrome (PTLS; MIM#610883). We successfully identified previously determined breakpoint junctions in three PTLS cases, and also were able to discover novel junctions in repetitive sequences, including LCR-mediated breakpoints. The new information has enabled us to propose mechanisms for formation of these structural variants. Conclusions The new method leverages the cost efficiency of targeted capture-sequencing as well as the mappability and scaffolding capabilities of long sequencing reads generated by the PacBio platform. It is therefore suitable for studying complex SVs, especially those involving LCRs, inversions, and the generation of chimeric Alu elements at the breakpoints. Other genomic research applications, such as haplotype phasing and small insertion and deletion validation could also benefit from this technology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1370-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Adam C English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Harsha V Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Fuli Yu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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Sawaya S, Boocock J, Black MA, Gemmell NJ. Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data. BMC Bioinformatics 2015; 16:21. [PMID: 25626999 PMCID: PMC4384361 DOI: 10.1186/s12859-014-0449-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 12/30/2014] [Indexed: 12/01/2022] Open
Abstract
Background Pausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA sequences. The Pacific Biosciences sequencer uses optics to view a polymerase and its interaction with a single DNA molecule in real-time, offering a unique way to detect potential alternative DNA structures. Results We have developed a new way to examine polymerase kinetics data and relate it to the DNA sequence by using a wavelet transform of read information from the sequencer. We use this method to examine how polymerase kinetics are related to nucleotide base composition. We then examine tandem repeat sequences known for their ability to form different DNA structures: (CGG)n and (CG)n repeats which can, respectively, form G-quadruplex DNA and Z-DNA. We find pausing around the (CGG)n repeat that may indicate the presence of G-quadruplexes in some of the sequencer reads. The (CG)n repeat does not appear to cause polymerase pausing, but its kinetics signature nevertheless suggests the possibility that alternative nucleotide conformations may sometimes be present. Conclusion We discuss the implications of using our method to discover DNA sequences capable of forming alternative structures. The analyses presented here can be reproduced on any Pacific Biosciences kinetics data for any DNA pattern of interest using an R package that we have made publicly available.
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Affiliation(s)
- Sterling Sawaya
- Institute for Behavioral Genetics, University of Colorado, Boulder, USA. .,Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
| | - James Boocock
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
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Rajan-Babu IS, Teo CRL, Lian M, Lee CG, Law HY, Chong SS. Single-tube methylation-specific duplex-PCR assay for rapid and accurate diagnosis ofFragile X Mental Retardation 1–related disorders. Expert Rev Mol Diagn 2015; 15:431-41. [DOI: 10.1586/14737159.2015.1001749] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wu Z, Gui S, Quan Z, Pan L, Wang S, Ke W, Liang D, Ding Y. A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots. BMC PLANT BIOLOGY 2014; 14:289. [PMID: 25407166 PMCID: PMC4245832 DOI: 10.1186/s12870-014-0289-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 10/15/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND The chloroplast genome is important for plant development and plant evolution. Nelumbo nucifera is one member of relict plants surviving from the late Cretaceous. Recently, a new sequencing platform PacBio RS II, known as 'SMRT (Single Molecule, Real-Time) sequencing', has been developed. Using the SMRT sequencing to investigate the chloroplast genome of N. nucifera will help to elucidate the plastid evolution of basal eudicots. RESULTS The sizes of the de novo assembled complete chloroplast genome of N. nucifera were 163,307 bp, 163,747 bp and 163,600 bp with average depths of coverage of 7×, 712× and 105× sequenced by Sanger, Illumina MiSeq and PacBio RS II, respectively. The precise chloroplast genome of N. nucifera was obtained from PacBio RS II data proofread by Illumina MiSeq reads, with a quadripartite structure containing a large single copy region (91,846 bp) and a small single copy region (19,626 bp) separated by two inverted repeat regions (26,064 bp). The genome contains 113 different genes, including four distinct rRNAs, 30 distinct tRNAs and 79 distinct peptide-coding genes. A phylogenetic analysis of 133 taxa from 56 orders indicated that Nelumbo with an age of 177 million years is a sister clade to Platanus, which belongs to the basal eudicots. Basal eudicots began to emerge during the early Jurassic with estimated divergence times at 197 million years using MCMCTree. IR expansions/contractions within the basal eudicots seem to have occurred independently. CONCLUSIONS Because of long reads and lack of bias in coverage of AT-rich regions, PacBio RS II showed a great promise for highly accurate 'finished' genomes, especially for a de novo assembly of genomes. N. nucifera is one member of basal eudicots, however, evolutionary analyses of IR structural variations of N. nucifera and other basal eudicots suggested that IR expansions/contractions occurred independently in these basal eudicots or were caused by independent insertions and deletions. The precise chloroplast genome of N. nucifera will present new information for structural variation of chloroplast genomes and provide new insight into the evolution of basal eudicots at the primary sequence and structural level.
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Affiliation(s)
- Zhihua Wu
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
| | - Songtao Gui
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
| | | | - Lei Pan
- />College of Life Sciences, Jianghan University, Wuhan, 430056 China
| | - Shuzhen Wang
- />College of Life Sciences, Huanggang Normal University, Huanggang, 438000 Hubei China
| | - Weidong Ke
- />Wuhan Vegetable Scientific Research Institute, Wuhan National Field Observation & Research Station for Aquatic Vegetables, Wuhan, 430065 China
| | - Dequan Liang
- />Nextomics Biosciences Co., Ltd., Wuhan, 430075 China
| | - Yi Ding
- />State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072 Republic of China
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Pretto DI, Eid JS, Yrigollen CM, Tang HT, Loomis EW, Raske C, Durbin-Johnson B, Hagerman PJ, Tassone F. Differential increases of specific FMR1 mRNA isoforms in premutation carriers. J Med Genet 2014; 52:42-52. [PMID: 25358671 DOI: 10.1136/jmedgenet-2014-102593] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Over 40% of male and ∼16% of female carriers of a premutation FMR1 allele (55-200 CGG repeats) will develop fragile X-associated tremor/ataxia syndrome, an adult onset neurodegenerative disorder, while about 20% of female carriers will develop fragile X-associated primary ovarian insufficiency. Marked elevation in FMR1 mRNA transcript levels has been observed with premutation alleles, and RNA toxicity due to increased mRNA levels is the leading molecular mechanism proposed for these disorders. However, although the FMR1 gene undergoes alternative splicing, it is unknown whether all or only some of the isoforms are overexpressed in premutation carriers and which isoforms may contribute to the premutation pathology. METHODS To address this question, we have applied a long-read sequencing approach using single-molecule real-time (SMRT) sequencing and qRT-PCR. RESULTS Our SMRT sequencing analysis performed on peripheral blood mononuclear cells, fibroblasts and brain tissue samples derived from premutation carriers and controls revealed the existence of 16 isoforms of 24 predicted variants. Although the relative abundance of all mRNA isoforms was significantly increased in the premutation group, as expected based on the bulk increase in mRNA levels, there was a disproportionate (fourfold to sixfold) increase, relative to the overall increase in mRNA, in the abundance of isoforms spliced at both exons 12 and 14, specifically Iso10 and Iso10b, containing the complete exon 15 and differing only in splicing in exon 17. CONCLUSIONS These findings suggest that RNA toxicity may arise from a relative increase of all FMR1 mRNA isoforms. Interestingly, the Iso10 and Iso10b mRNA isoforms, lacking the C-terminal functional sites for fragile X mental retardation protein function, are the most increased in premutation carriers relative to normal, suggesting a functional relevance in the pathology of FMR1-associated disorders.
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Affiliation(s)
- Dalyir I Pretto
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - John S Eid
- Pacific Biosciences, Menlo Park, California, USA
| | - Carolyn M Yrigollen
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Hiu-Tung Tang
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Erick W Loomis
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Chris Raske
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA
| | - Blythe Durbin-Johnson
- Department of Public Health Sciences, University of California Davis, School of Medicine, Davis, California, USA
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA MIND Institute, University of California Davis Medical Center, Sacramento, California, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California, USA MIND Institute, University of California Davis Medical Center, Sacramento, California, USA
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Buermans H, den Dunnen J. Next generation sequencing technology: Advances and applications. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1932-1941. [DOI: 10.1016/j.bbadis.2014.06.015] [Citation(s) in RCA: 460] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 06/05/2014] [Accepted: 06/15/2014] [Indexed: 12/12/2022]
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Li W, Freudenberg J. Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. Comput Biol Chem 2014; 53 Pt A:108-17. [PMID: 25241312 DOI: 10.1016/j.compbiolchem.2014.08.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 12/31/2022]
Abstract
Repetitive and redundant regions of a genome are particularly problematic for mapping sequencing reads. In the present paper, we compile a list of the unmappable regions in the human genome based on the following definition: hypothetical reads with length 1 kb which cannot be uniquely mapped with zero-mismatch alignment for the described regions, considering both the forward and reverse strand. The respective collection of unmappable regions covers 0.77% of the sequence of human autosomes and 8.25% of the sex chromosomes in the reference genome GRCh37/hg19 (overall 1.23%). Not surprisingly, our unmappable regions overlap greatly with segmental duplication, transposable elements, and structural variants. About 99.8% of bases in our unmappable regions are part of either segmental duplication or transposable elements and 98.3% overlap structural variant annotations. Notably, some of these regions overlap units with important biological functions, including 4% of protein-coding genes. In contrast, these regions have zero intersection with the ultraconserved elements, very low overlap with microRNAs, tRNAs, pseudogenes, CpG islands, tandem repeats, microsatellites, sensitive non-coding regions, and the mapping blacklist regions from the ENCODE project.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, 350 Community Drive, Manhasset, NY 11030, USA.
| | - Jan Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, 350 Community Drive, Manhasset, NY 11030, USA
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Sequence alignment tools: one parallel pattern to rule them all? BIOMED RESEARCH INTERNATIONAL 2014; 2014:539410. [PMID: 25147803 PMCID: PMC4131566 DOI: 10.1155/2014/539410] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 06/03/2014] [Accepted: 06/21/2014] [Indexed: 11/17/2022]
Abstract
In this paper, we advocate high-level programming methodology for next generation sequencers (NGS) alignment tools for both productivity and absolute performance. We analyse the problem of parallel alignment and review the parallelisation strategies of the most popular alignment tools, which can all be abstracted to a single parallel paradigm. We compare these tools to their porting onto the FastFlow pattern-based programming framework, which provides programmers with high-level parallel patterns. By using a high-level approach, programmers are liberated from all complex aspects of parallel programming, such as synchronisation protocols, and task scheduling, gaining more possibility for seamless performance tuning. In this work, we show some use cases in which, by using a high-level approach for parallelising NGS tools, it is possible to obtain comparable or even better absolute performance for all used datasets.
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127
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Hackl T, Hedrich R, Schultz J, Förster F. proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. ACTA ACUST UNITED AC 2014; 30:3004-11. [PMID: 25015988 DOI: 10.1093/bioinformatics/btu392] [Citation(s) in RCA: 321] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MOTIVATION Today, the base code of DNA is mostly determined through sequencing by synthesis as provided by the Illumina sequencers. Although highly accurate, resulting reads are short, making their analyses challenging. Recently, a new technology, single molecule real-time (SMRT) sequencing, was developed that could address these challenges, as it generates reads of several thousand bases. But, their broad application has been hampered by a high error rate. Therefore, hybrid approaches that use high-quality short reads to correct erroneous SMRT long reads have been developed. Still, current implementations have great demands on hardware, work only in well-defined computing infrastructures and reject a substantial amount of reads. This limits their usability considerably, especially in the case of large sequencing projects. RESULTS Here we present proovread, a hybrid correction pipeline for SMRT reads, which can be flexibly adapted on existing hardware and infrastructure from a laptop to a high-performance computing cluster. On genomic and transcriptomic test cases covering Escherichia coli, Arabidopsis thaliana and human, proovread achieved accuracies up to 99.9% and outperformed the existing hybrid correction programs. Furthermore, proovread-corrected sequences were longer and the throughput was higher. Thus, proovread combines the most accurate correction results with an excellent adaptability to the available hardware. It will therefore increase the applicability and value of SMRT sequencing. AVAILABILITY AND IMPLEMENTATION proovread is available at the following URL: http://proovread.bioapps.biozentrum.uni-wuerzburg.de.
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Affiliation(s)
- Thomas Hackl
- Department for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany and Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany Department for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany and Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Rainer Hedrich
- Department for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany and Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Jörg Schultz
- Department for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany and Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Frank Förster
- Department for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany and Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
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English AC, Salerno WJ, Reid JG. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinformatics 2014; 15:180. [PMID: 24915764 PMCID: PMC4082283 DOI: 10.1186/1471-2105-15-180] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/04/2014] [Indexed: 11/25/2022] Open
Abstract
Background As resequencing projects become more prevalent across a larger number of species, accurate variant identification will further elucidate the nature of genetic diversity and become increasingly relevant in genomic studies. However, the identification of larger genomic variants via DNA sequencing is limited by both the incomplete information provided by sequencing reads and the nature of the genome itself. Long-read sequencing technologies provide high-resolution access to structural variants often inaccessible to shorter reads. Results We present PBHoney, software that considers both intra-read discordance and soft-clipped tails of long reads (>10,000 bp) to identify structural variants. As a proof of concept, we identify four structural variants and two genomic features in a strain of Escherichia coli with PBHoney and validate them via de novo assembly. PBHoney is available for download at http://sourceforge.net/projects/pb-jelly/. Conclusions Implementing two variant-identification approaches that exploit the high mappability of long reads, PBHoney is demonstrated as being effective at detecting larger structural variants using whole-genome Pacific Biosciences RS II Continuous Long Reads. Furthermore, PBHoney is able to discover two genomic features: the existence of Rac-Phage in isolate; evidence of E. coli’s circular genome.
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Affiliation(s)
- Adam C English
- Human Genome Sequencing Center at Baylor College of Medicine, One Baylor Plaza, Houston 77030, Texas, USA.
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Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G. A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol 2014; 31:872-88. [PMID: 24425782 PMCID: PMC3969562 DOI: 10.1093/molbev/msu037] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies.
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Affiliation(s)
- Anders Bergström
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | | | - Francisco Salinas
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | - Benjamin Barré
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | - Leopold Parts
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Amin Zia
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine
| | - Alex N. Nguyen Ba
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Alan M. Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Edward J. Louis
- Centre of Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | - Ville Mustonen
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Richard Durbin
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Gianni Liti
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
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Hendel A, Kildebeck EJ, Fine EJ, Clark J, Punjya N, Sebastiano V, Bao G, Porteus MH. Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. Cell Rep 2014; 7:293-305. [PMID: 24685129 DOI: 10.1016/j.celrep.2014.02.040] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/16/2014] [Accepted: 02/26/2014] [Indexed: 12/19/2022] Open
Abstract
Targeted genome editing with engineered nucleases has transformed the ability to introduce precise sequence modifications at almost any site within the genome. A major obstacle to probing the efficiency and consequences of genome editing is that no existing method enables the frequency of different editing events to be simultaneously measured across a cell population at any endogenous genomic locus. We have developed a method for quantifying individual genome-editing outcomes at any site of interest with single-molecule real-time (SMRT) DNA sequencing. We show that this approach can be applied at various loci using multiple engineered nuclease platforms, including transcription-activator-like effector nucleases (TALENs), RNA-guided endonucleases (CRISPR/Cas9), and zinc finger nucleases (ZFNs), and in different cell lines to identify conditions and strategies in which the desired engineering outcome has occurred. This approach offers a technique for studying double-strand break repair, facilitates the evaluation of gene-editing technologies, and permits sensitive quantification of editing outcomes in almost every experimental system used.
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Affiliation(s)
- Ayal Hendel
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Eric J Kildebeck
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Eli J Fine
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Joseph Clark
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Niraj Punjya
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Vittorio Sebastiano
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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131
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Abstract
Genomic data have become commonplace in most branches of the biological sciences and have fundamentally altered the way research is conducted. However, the predominance of short-read sequence data from second-generation sequencing technologies has commonly resulted in fragmented and partial genomic data characteristics. In this opinion, I will highlight how long, unbiased reads from single molecule, real-time (SMRT) sequencing now allow for a return to more contiguous and comprehensive views of genomes.
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Affiliation(s)
- Jonas Korlach
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, United States
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132
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Abstract
Genetics has been revolutionised by recent technologies. The latest addition to these advances is next-generation sequencing, which is set to transform clinical diagnostics in every branch of medicine. In the research arena this has already been instrumental in identifying hundreds of novel genetic syndromes, making a molecular diagnosis possible for the first time in numerous refractory cases. However, the pace of change has left many clinicians bewildered by new terminology and the implications of next-generation sequencing for their clinical practice. The rapid developments have also left many diagnostic laboratories struggling to implement these new technologies with limited resources. This review explains the basic concepts of next-generation sequencing, gives examples of its role in clinically applied research and examines the challenges of its introduction into clinical practice.
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133
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Performance of high-throughput sequencing for the discovery of genetic variation across the complete size spectrum. G3-GENES GENOMES GENETICS 2014; 4:63-5. [PMID: 24192839 PMCID: PMC3887540 DOI: 10.1534/g3.113.008797] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We observed that current high-throughput sequencing approaches only detected a fraction of the full size-spectrum of insertions, deletions, and copy number variants compared with a previously published, Sanger-sequenced human genome. The sensitivity for detection was the lowest in the 100- to 10,000-bp size range, and at DNA repeats, with copy number gains harder to delineate than losses. We discuss strategies for discovering the full spectrum of genetic variation necessary for disease association studies.
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134
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135
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Doi K, Monjo T, Hoang PH, Yoshimura J, Yurino H, Mitsui J, Ishiura H, Takahashi Y, Ichikawa Y, Goto J, Tsuji S, Morishita S. Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing. ACTA ACUST UNITED AC 2013; 30:815-22. [PMID: 24215022 PMCID: PMC3957077 DOI: 10.1093/bioinformatics/btt647] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Motivation: Long expansions of short tandem repeats (STRs), i.e. DNA repeats of 2–6 nt, are associated with some genetic diseases. Cost-efficient high-throughput sequencing can quickly produce billions of short reads that would be useful for uncovering disease-associated STRs. However, enumerating STRs in short reads remains largely unexplored because of the difficulty in elucidating STRs much longer than 100 bp, the typical length of short reads. Results: We propose ab initio procedures for sensing and locating long STRs promptly by using the frequency distribution of all STRs and paired-end read information. We validated the reproducibility of this method using biological replicates and used it to locate an STR associated with a brain disease (SCA31). Subsequently, we sequenced this STR site in 11 SCA31 samples using SMRTTM sequencing (Pacific Biosciences), determined 2.3–3.1 kb sequences at nucleotide resolution and revealed that (TGGAA)- and (TAAAATAGAA)-repeat expansions determined the instability of the repeat expansions associated with SCA31. Our method could also identify common STRs, (AAAG)- and (AAAAG)-repeat expansions, which are remarkably expanded at four positions in an SCA31 sample. This is the first proposed method for rapidly finding disease-associated long STRs in personal genomes using hybrid sequencing of short and long reads. Availability and implementation: Our TRhist software is available at http://trhist.gi.k.u-tokyo.ac.jp/. Contact:moris@cb.k.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Koichiro Doi
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Department of Information and Communication Engineering, Faculty of Engineering and Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
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136
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Evans-Galea MV, Hannan AJ, Carrodus N, Delatycki MB, Saffery R. Epigenetic modifications in trinucleotide repeat diseases. Trends Mol Med 2013; 19:655-63. [DOI: 10.1016/j.molmed.2013.07.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/12/2013] [Accepted: 07/22/2013] [Indexed: 12/18/2022]
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137
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Zhang W, Ciclitira P, Messing J. PacBio sequencing of gene families - a case study with wheat gluten genes. Gene 2013; 533:541-6. [PMID: 24144842 DOI: 10.1016/j.gene.2013.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 10/03/2013] [Indexed: 12/16/2022]
Abstract
Amino acids in wheat (Triticum aestivum) seeds mainly accumulate in storage proteins called gliadins and glutenins. Gliadins contain α/β-, γ- and ω-types whereas glutenins contain HMW- and LMW-types. Known gliadin and glutenin sequences were largely determined through cloning and sequencing by capillary electrophoresis. This time-consuming process prevents us to intensively study the variation of each orthologous gene copy among cultivars. The throughput and sequencing length of Pacific Bioscience RS (PacBio) single molecule sequencing platform make it feasible to construct contiguous and non-chimeric RNA sequences. We assembled 424 wheat storage protein transcripts from ten wheat cultivars by using just one single-molecule-real-time cell. The protein genes from wheat cultivar Chinese Spring are comparable to known sequences from NCBI. We demonstrated real-time sequencing of gene families with high-throughput and low-cost. This method can be applied to studies of gene amplification and copy number variation among species and cultivars.
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Affiliation(s)
- Wei Zhang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
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138
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Németh AH, Kwasniewska AC, Lise S, Parolin Schnekenberg R, Becker EBE, Bera KD, Shanks ME, Gregory L, Buck D, Zameel Cader M, Talbot K, de Silva R, Fletcher N, Hastings R, Jayawant S, Morrison PJ, Worth P, Taylor M, Tolmie J, O’Regan M, Valentine R, Packham E, Evans J, Seller A, Ragoussis J. Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model. Brain 2013; 136:3106-18. [PMID: 24030952 PMCID: PMC3784284 DOI: 10.1093/brain/awt236] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/28/2013] [Accepted: 06/20/2013] [Indexed: 12/23/2022] Open
Abstract
Many neurological conditions are caused by immensely heterogeneous gene mutations. The diagnostic process is often long and complex with most patients undergoing multiple invasive and costly investigations without ever reaching a conclusive molecular diagnosis. The advent of massively parallel, next-generation sequencing promises to revolutionize genetic testing and shorten the 'diagnostic odyssey' for many of these patients. We performed a pilot study using heterogeneous ataxias as a model neurogenetic disorder to assess the introduction of next-generation sequencing into clinical practice. We captured 58 known human ataxia genes followed by Illumina Next-Generation Sequencing in 50 highly heterogeneous patients with ataxia who had been extensively investigated and were refractory to diagnosis. All cases had been tested for spinocerebellar ataxia 1-3, 6, 7 and Friedrich's ataxia and had multiple other biochemical, genetic and invasive tests. In those cases where we identified the genetic mutation, we determined the time to diagnosis. Pathogenicity was assessed using a bioinformatics pipeline and novel variants were validated using functional experiments. The overall detection rate in our heterogeneous cohort was 18% and varied from 8.3% in those with an adult onset progressive disorder to 40% in those with a childhood or adolescent onset progressive disorder. The highest detection rate was in those with an adolescent onset and a family history (75%). The majority of cases with detectable mutations had a childhood onset but most are now adults, reflecting the long delay in diagnosis. The delays were primarily related to lack of easily available clinical testing, but other factors included the presence of atypical phenotypes and the use of indirect testing. In the cases where we made an eventual diagnosis, the delay was 3-35 years (mean 18.1 years). Alignment and coverage metrics indicated that the capture and sequencing was highly efficient and the consumable cost was ∼£400 (€460 or US$620). Our pathogenicity interpretation pathway predicted 13 different mutations in eight different genes: PRKCG, TTBK2, SETX, SPTBN2, SACS, MRE11, KCNC3 and DARS2 of which nine were novel including one causing a newly described recessive ataxia syndrome. Genetic testing using targeted capture followed by next-generation sequencing was efficient, cost-effective, and enabled a molecular diagnosis in many refractory cases. A specific challenge of next-generation sequencing data is pathogenicity interpretation, but functional analysis confirmed the pathogenicity of novel variants showing that the pipeline was robust. Our results have broad implications for clinical neurology practice and the approach to diagnostic testing.
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Affiliation(s)
- Andrea H. Németh
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- 2 Department of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 7LJ, UK
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Alexandra C. Kwasniewska
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Stefano Lise
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Ricardo Parolin Schnekenberg
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
- 4 School of Medicine, Universidade Positivo, Curitiba, Brazil
| | - Esther B. E. Becker
- 5 Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, OX1 3QX, UK
| | - Katarzyna D. Bera
- 5 Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, OX1 3QX, UK
| | - Morag E. Shanks
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - Lorna Gregory
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - David Buck
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
| | - M. Zameel Cader
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Kevin Talbot
- 1 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Rajith de Silva
- 6 Department of Neurology, Essex Centre for Neurological Sciences, Queen's Hospital, Romford, UK
| | | | - Rob Hastings
- 8 Department of Clinical Genetics, St Michael's Hospital, Bristol, BS2 8EG, UK
| | - Sandeep Jayawant
- 9 Department of Paediatrics, Oxford University Hospitals NHS Trust, Oxford, OX3 7LJ, UK
| | - Patrick J. Morrison
- 10 School of Medicine, Dentistry and Biomedical Sciences, Queens University, Belfast, BT9 7BL, Northern Ireland, UK
| | - Paul Worth
- 11 Department of Neurology, Norfolk and Norwich University Hospital, Norwich, UK
| | - Malcolm Taylor
- 12 School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - John Tolmie
- 13 Department of Clinical Genetics, Southern General Hospital, Glasgow G51 4TF, UK
| | - Mary O’Regan
- 14 Fraser of Allander Neurosciences Unit, Royal Hospital for Sick Children, Glasgow G3 8SJ, UK
| | | | - Ruth Valentine
- 15 Thames Valley Dementia and Neurodegenerative Diseases Network, Oxford, UK
| | - Emily Packham
- 16 Oxford Regional Molecular Genetics Laboratories, Oxford University Hospitals NHS Trust
| | - Julie Evans
- 16 Oxford Regional Molecular Genetics Laboratories, Oxford University Hospitals NHS Trust
| | - Anneke Seller
- 16 Oxford Regional Molecular Genetics Laboratories, Oxford University Hospitals NHS Trust
| | - Jiannis Ragoussis
- 3 Wellcome Trust Centre for Human Genetics, University of Oxford, OX3 7BN, UK
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139
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Gong X, Zhang K, Wang Y, Wang J, Cui Y, Li S, Luo Y. MicroRNA-130b targets Fmr1 and regulates embryonic neural progenitor cell proliferation and differentiation. Biochem Biophys Res Commun 2013; 439:493-500. [PMID: 24021279 DOI: 10.1016/j.bbrc.2013.08.096] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 11/17/2022]
Abstract
Fragile X syndrome, one of the most common forms of inherited mental retardation, is caused by expansion of the CGG repeat in the 5'-untranslated region of the X-linked Fmr1 gene, which results in transcriptional silencing and loss of expression of its encoded protein FMRP. The loss of FMRP increases proliferation and alters fate specification in adult neural progenitor cells (aNPCs). However, little is known about Fmr1 mRNA regulation at the transcriptional and post-transcriptional levels. In the present study, we report that miR-130b regulated Fmr1 expression by directly targeting its 3'-untranslated region (3' UTR). Up-regulation of miR-130b in mouse embryonic neural progenitor cells (eNPCs) decreased Fmr1 expression, markedly increased eNPC proliferation and altered the differentiation tendency of eNPCs, suggesting that antagonizing miR-130b may be a new therapeutic entry point for treating Fragile X syndrome.
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Affiliation(s)
- Xi Gong
- State Key Laboratory of Food Science and Technology, College of Life Sciences and Food Engineering, Nanchang University, Nanchang 330047, China
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140
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Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563-9. [PMID: 23644548 DOI: 10.1038/nmeth.2474] [Citation(s) in RCA: 3150] [Impact Index Per Article: 286.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/04/2013] [Indexed: 02/08/2023]
Abstract
We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.
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141
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Next-generation sequencing for preimplantation genetic diagnosis. Fertil Steril 2013; 99:e17-8. [DOI: 10.1016/j.fertnstert.2013.02.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 01/22/2023]
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142
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Next-generation sequencing diagnostics for neurological diseases/disorders: from a clinical perspective. Hum Genet 2013; 132:721-34. [PMID: 23525706 DOI: 10.1007/s00439-013-1287-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/02/2013] [Indexed: 12/13/2022]
Abstract
Neurological diseases encompass a broad, heterogeneous group of disorders ranging from pediatric neurodevelopmental diseases to late-onset neurodegenerative diseases, most of which are poorly understood and few of which are curable. Most of these diseases have a genetic basis and thus are expected to be amenable to genetic or genomic analysis by next-generation sequencing (NGS). While the advancement of contemporary technologies (such as NGS) is exciting, translating this tool into actual benefit for patients and clinicians can be challenging. In a clinical setting, a sequencing test that is fast, non-invasive, cheap and with perfect specificity would be ideal. However, in practice, there are several hurdles and caveats to consider even before a NGS diagnostic testing can be optimally applied. Proper definition of clinical phenotype, selection of the most appropriate subjects and the clinical setting, optimization of both sensitivity and specificity of the test, evaluation of the availability of the infrastructure and expertise, and consideration of economic, ethical and legal issues are vital in the final application of NGS diagnostic screening in the clinics.
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143
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Savić Pavićević D, Miladinović J, Brkušanin M, Šviković S, Djurica S, Brajušković G, Romac S. Molecular genetics and genetic testing in myotonic dystrophy type 1. BIOMED RESEARCH INTERNATIONAL 2013; 2013:391821. [PMID: 23586035 PMCID: PMC3613064 DOI: 10.1155/2013/391821] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/05/2013] [Indexed: 12/29/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is the most common adult onset muscular dystrophy, presenting as a multisystemic disorder with extremely variable clinical manifestation, from asymptomatic adults to severely affected neonates. A striking anticipation and parental-gender effect upon transmission are distinguishing genetic features in DM1 pedigrees. It is an autosomal dominant hereditary disease associated with an unstable expansion of CTG repeats in the 3'-UTR of the DMPK gene, with the number of repeats ranging from 50 to several thousand. The number of CTG repeats broadly correlates with both the age-at-onset and overall severity of the disease. Expanded DM1 alleles are characterized by a remarkable expansion-biased and gender-specific germline instability, and tissue-specific, expansion-biased, age-dependent, and individual-specific somatic instability. Mutational dynamics in male and female germline account for observed anticipation and parental-gender effect in DM1 pedigrees, while mutational dynamics in somatic tissues contribute toward the tissue-specificity and progressive nature of the disease. Genetic test is routinely used in diagnostic procedure for DM1 for symptomatic, asymptomatic, and prenatal testing, accompanied with appropriate genetic counseling and, as recommended, without predictive information about the disease course. We review molecular genetics of DM1 with focus on those issues important for genetic testing and counseling.
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Affiliation(s)
- Dušanka Savić Pavićević
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, P.O. Box 52, 11000 Belgrade, Serbia
| | - Jelena Miladinović
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, P.O. Box 52, 11000 Belgrade, Serbia
| | - Miloš Brkušanin
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, P.O. Box 52, 11000 Belgrade, Serbia
| | - Saša Šviković
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, P.O. Box 52, 11000 Belgrade, Serbia
| | - Svetlana Djurica
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, P.O. Box 52, 11000 Belgrade, Serbia
| | - Goran Brajušković
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, P.O. Box 52, 11000 Belgrade, Serbia
| | - Stanka Romac
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, P.O. Box 52, 11000 Belgrade, Serbia
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144
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Korlach J. Single Molecule, Real-Time DNA Sequencing Yields a Clearer Picture of Biological Complexity: Helps Scientists Close Genomes, Study Linked Variants, and Detect Base Modifications. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.1546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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