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Puthenpura V, DeNunzio NJ, Zeng X, Giantsoudi D, Aboian M, Ebb D, Kahle KT, Yock TI, Marks AM. Radiation Necrosis with Proton Therapy in a Patient with Aarskog-Scott Syndrome and Medulloblastoma. Int J Part Ther 2021; 8:58-65. [PMID: 35127977 PMCID: PMC8768897 DOI: 10.14338/ijpt-21-00013.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/18/2021] [Indexed: 11/21/2022] Open
Abstract
Purpose Medulloblastoma is known to be associated with multiple cancer-predisposition syndromes. In this article, we explore a possible association among a patient's Aarskog-Scott syndrome, development of medulloblastoma, and subsequent brainstem radiation necrosis. Case Presentation A 5-year-old male with Aarskog-Scott syndrome initially presented to his pediatrician with morning emesis, gait instability, and truncal weakness. He was ultimately found to have a posterior fossa tumor with pathology consistent with group 3 medulloblastoma. After receiving a gross total resection and standard proton beam radiation therapy with concurrent vincristine, he was noted to develop brainstem radiation necrosis, for which he underwent therapy with high-dose dexamethasone, bevacizumab, and hyperbaric oxygen therapy with radiographic improvement and clinical stabilization. Conclusion Based on several possible pathologic correlates in the FDG1 pathway, there exists a potential association between this patient's Aarskog-Scott syndrome and medulloblastoma, which needs to be investigated further. In patients with underlying, rare genetic syndromes, further caution should be taken when evaluating chemotherapy and radiation dosimetry planning.
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Affiliation(s)
- Vidya Puthenpura
- Section of Pediatric Hematology and Oncology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Nicholas J. DeNunzio
- Department of Radiation Oncology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Xue Zeng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Drosoula Giantsoudi
- Department of Radiation Oncology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Mariam Aboian
- Section of Neuroradiology and Nuclear Medicine, Department of Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - David Ebb
- Department of Pediatric Hematology/Oncology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Kristopher T. Kahle
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Torunn I. Yock
- Department of Radiation Oncology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Asher M. Marks
- Section of Pediatric Hematology and Oncology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
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conLSH: Context based Locality Sensitive Hashing for mapping of noisy SMRT reads. Comput Biol Chem 2020; 85:107206. [PMID: 32000034 DOI: 10.1016/j.compbiolchem.2020.107206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/14/2020] [Indexed: 11/20/2022]
Abstract
Single Molecule Real-Time (SMRT) sequencing is a recent advancement of Next Gen technology developed by Pacific Bio (PacBio). It comes with an explosion of long and noisy reads demanding cutting edge research to get most out of it. To deal with the high error probability of SMRT data, a novel contextual Locality Sensitive Hashing (conLSH) based algorithm is proposed in this article, which can effectively align the noisy SMRT reads to the reference genome. Here, sequences are hashed together based not only on their closeness, but also on similarity of context. The algorithm has O(nρ+1) space requirement, where n is the number of sequences in the corpus and ρ is a constant. The indexing time and querying time are bounded by Onρ+1·lnnln1P2 and O(nρ) respectively, where P2 > 0, is a probability value. This algorithm is particularly useful for retrieving similar sequences, a widely used task in biology. The proposed conLSH based aligner is compared with rHAT, popularly used for aligning SMRT reads, and is found to comprehensively beat it in speed as well as in memory requirements. In particular, it takes approximately 24.2% less processing time, while saving about 70.3% in peak memory requirement for H.sapiens PacBio dataset.
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The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Sci Rep 2019; 9:9354. [PMID: 31249361 PMCID: PMC6597582 DOI: 10.1038/s41598-019-45839-z] [Citation(s) in RCA: 714] [Impact Index Per Article: 142.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/13/2019] [Indexed: 12/31/2022] Open
Abstract
Functional genomics assays based on high-throughput sequencing greatly expand our ability to understand the genome. Here, we define the ENCODE blacklist- a comprehensive set of regions in the human, mouse, worm, and fly genomes that have anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment. The removal of the ENCODE blacklist is an essential quality measure when analyzing functional genomics data.
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Non-invasive prenatal testing as a valuable source of population specific allelic frequencies. J Biotechnol 2019; 299:72-78. [PMID: 31054297 DOI: 10.1016/j.jbiotec.2019.04.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/30/2022]
Abstract
Low-coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT) of common aneuploidies is one of the most rapidly adopted and relatively low-cost DNA tests. Since aggregation of reads from a large number of samples allows overcoming the problems of extremely low coverage of individual samples, we describe the possible re-use of the data generated during NIPT testing for genome scale population specific frequency determination of small DNA variants, requiring no additional costs except of those for the NIPT test itself. We applied our method to a data set comprising of 1501 original NIPT test results and evaluated the findings on different levels, from in silico population frequency comparisons up to wet lab validation analyses using a gold-standard method based on Sanger sequencing. The revealed high reliability of variant calling and allelic frequency determinations suggest that these NIPT data could serve as valuable alternatives to large scale population studies even for smaller countries around the world.
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Kubiritova Z, Gyuraszova M, Nagyova E, Hyblova M, Harsanyova M, Budis J, Hekel R, Gazdarica J, Duris F, Kadasi L, Szemes T, Radvanszky J. On the critical evaluation and confirmation of germline sequence variants identified using massively parallel sequencing. J Biotechnol 2019; 298:64-75. [PMID: 30998956 DOI: 10.1016/j.jbiotec.2019.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 12/30/2022]
Abstract
Although massively parallel sequencing (MPS) is becoming common practice in both research and routine clinical care, confirmation requirements of identified DNA variants using alternative methods are still topics of debate. When evaluating variants directly from MPS data, different read depth statistics, together with specialized genotype quality scores are, therefore, of high relevance. Here we report results of our validation study performed in two different ways: 1) confirmation of MPS identified variants using Sanger sequencing; and 2) simultaneous Sanger and MPS analysis of exons of selected genes. Detailed examination of false-positive and false-negative findings revealed typical error sources connected to low read depth/coverage, incomplete reference genome, indel realignment problems, as well as microsatellite associated amplification errors leading to base miss-calling. However, all these error types were identifiable with thorough manual revision of aligned reads according to specific patterns of distributions of variants and their corresponding reads. Moreover, our results point to dependence of both basic quantitative metrics (such as total read counts, alternative allele read counts and allelic balance) together with specific genotype quality scores on the used bioinformatics pipeline, stressing thus the need for establishing of specific thresholds for these metrics in each laboratory and for each involved pipeline independently.
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Affiliation(s)
- Zuzana Kubiritova
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Marianna Gyuraszova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Emilia Nagyova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Department of Cardiology, Division Heart & Lungs, UMC Utrecht, University of Utrecht, the Netherlands
| | - Michaela Hyblova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia
| | - Maria Harsanyova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia
| | - Jaroslav Budis
- Geneton Ltd., Bratislava, Slovakia; Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Rastislav Hekel
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Juraj Gazdarica
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Frantisek Duris
- Geneton Ltd., Bratislava, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Ludevit Kadasi
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia
| | - Jan Radvanszky
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia.
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Li W, Freudenberg J, Freudenberg J. Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome. Gene 2019; 691:141-152. [PMID: 30630097 DOI: 10.1016/j.gene.2018.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
Abstract
The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a "Manhattan plot" style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
| | - Jerome Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Jan Freudenberg
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
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Chu TS, Liu BT. Establishing new mechanisms with triplet and singlet excited-state hydrogen bonding roles in photoinduced liquid dynamics. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1148450] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Misas E, Muñoz JF, Gallo JE, McEwen JG, Clay OK. From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity. Comput Biol Chem 2016; 61:258-69. [PMID: 26970210 DOI: 10.1016/j.compbiolchem.2016.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 02/03/2016] [Accepted: 02/16/2016] [Indexed: 01/26/2023]
Abstract
The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assemblies. Fungal mitochondrial (mtDNA) genomes are compact (typically less than 100 kb), yet often contain short non-unique sequences that can be shown to impede their successful de novo assembly in silico. Such repeats can also confuse processes in the cell in vivo. A well-studied example is ectopic (out-of-register, illegitimate) recombination associated with repeat pairs, which can lead to deletion of functionally important genes that are located between the repeats. Repeats that remain conserved over micro- or macroevolutionary timescales despite such risks may indicate functionally or structurally (e.g., for replication) important regions. This principle could form the basis of a mining strategy for accelerating discovery of function in genome sequences. We present here our screening of a sample of 11 fully sequenced fungal mitochondrial genomes by observing where exact k-mer repeats occurred several times; initial analyses motivated us to focus on 17-mers occurring more than three times. Based on the diverse repeats we observe, we propose that such screening may serve as an efficient expedient for gaining a rapid but representative first insight into the repeat landscapes of sparsely characterized mitochondrial chromosomes. Our matching of the flagged repeats to previously reported regions of interest supports the idea that systems of persisting, non-trivial repeats in genomes can often highlight features meriting further attention.
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Affiliation(s)
- Elizabeth Misas
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - José Fernando Muñoz
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Juan Esteban Gallo
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan Guillermo McEwen
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Oliver Keatinge Clay
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia.
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Abstract
As a result of multiple technological and practical advances, high-throughput sequencing, known more commonly as “next-generation” sequencing (NGS), can now be incorporated into standard clinical practice. Whereas early protocols relied on samples that were harvested outside of typical clinical pathology workflows, standard formalin-fixed, paraffin-embedded specimens can more regularly be used as starting materials for NGS. Furthermore, protocols for the analysis and interpretation of NGS data, as well as knowledge bases, are being amassed, allowing clinicians to act more easily on genomic information at the point of care for patients. In parallel, new therapies that target somatically mutated genes identified through clinical NGS are gaining US Food and Drug Administration (FDA) approval, and novel clinical trial designs are emerging in which genetic identifiers are given equal weight to histology. For clinical oncology providers, understanding the potential and the limitations of DNA sequencing will be crucial for providing genomically driven care in this era of precision medicine.
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Affiliation(s)
- Jeffrey Gagan
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115 USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ; Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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11
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Abstract
Power-law distributions are the main functional form for the distribution of repeat size and repeat copy number in the human genome. When the genome is broken into fragments for sequencing, the limited size of fragments and reads may prevent an unique alignment of repeat sequences to the reference sequence. Repeats in the human genome can be as long as 104 bases, or 105 − 106 bases when allowing for mismatches between repeat units. Sequence reads from these regions are therefore unmappable when the read length is in the range of 103 bases. With a read length of 1000 bases, slightly more than 1% of the assembled genome, and slightly less than 1% of the 1 kb reads, are unmappable, excluding the unassembled portion of the human genome (8% in GRCh37/hg19). The slow decay (long tail) of the power-law function implies a diminishing return in converting unmappable regions/reads to become mappable with the increase of the read length, with the understanding that increasing read length will always move toward the direction of 100% mappability.
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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 Manhasset, NY, USA
| | - Jan Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System Manhasset, NY, USA
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