Variant calling and benchmarking in an era of complete human genome sequences

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(7), P. 464 - 483

Published: April 14, 2023

Language: Английский

---

Mechanisms of structural chromosomal rearrangement formation

Molecular Cytogenetics, Journal Year: 2022, Volume and Issue: 15(1)

Published: June 14, 2022

Abstract Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead genetic instability. Most these arise recombination, repair, or replication occur after a double-strand break the stalling/breakage fork. Here, we review formation structural rearrangements, highlighting their main and differences. The most important constitutional alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling Template Switching (FoSTeS), Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis complex inverted duplications associated with terminal deletions, ring chromosomes is also outlined. We reinforce importance high-resolution analysis determine DNA sequence at, near, breakpoints order infer reveal how cells respond damage repair broken ends.

Language: Английский

---

Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(7), P. 476 - 499

Published: March 11, 2024

Language: Английский

---

High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance

Leukemia, Journal Year: 2022, Volume and Issue: 36(9), P. 2306 - 2316

Published: Aug. 1, 2022

Chromosome banding analysis (CBA) remains the standard-of-care for structural variant (SV) assessment in MDS. Optical genome mapping (OGM) is a novel, non-sequencing-based technique high-resolution genome-wide SV profiling (SVP). We explored clinical value of SVP by OGM 101 consecutive, newly diagnosed MDS patients from single-center, who underwent cytogenetic and targeted NGS studies. detected 383 clinically significant, recurrent novel SVs. Of these, 224 (51%) SVs, seen across 34% patients, were cryptic CBA (included rearrangements involving MECOM, NUP98::PRRX2, KMT2A partial tandem duplications among others). decreased proportion normal karyotype 16%, identified complex genomes (17%), chromothripsis (6%) generated informative results both with insufficient metaphases. Precise gene/exon-level allowed relevant biomarkers (TP53 allele status, KMT2A-PTD) without additional testing. data was complementary to NGS. When applied retrospect, changed comprehensive scoring system (CCSS) R-IPSS risk-groups 21% 17% respectively an improved prediction prognosis. By multivariate analysis, CCSS only (not CBA), TP53 mutation BM blasts independently predicted survival. This first largest study reporting combined prognostication.

Language: Английский

---

Familial long-read sequencing increases yield of de novo mutations

The American Journal of Human Genetics, Journal Year: 2022, Volume and Issue: 109(4), P. 631 - 646

Published: March 14, 2022

Language: Английский

---

How to proceed after “negative” exome: A review on genetic diagnostics, limitations, challenges, and emerging new multiomics techniques

Journal of Inherited Metabolic Disease, Journal Year: 2022, Volume and Issue: 45(4), P. 663 - 681

Published: May 4, 2022

Language: Английский

---

The consequences of recurrent genetic and epigenetic variants in human pluripotent stem cells

Cell stem cell, Journal Year: 2022, Volume and Issue: 29(12), P. 1624 - 1636

Published: Dec. 1, 2022

Language: Английский

---

Optical genome mapping reveals additional prognostic information compared to conventional cytogenetics in AML/MDS patients

International Journal of Cancer, Journal Year: 2022, Volume and Issue: 150(12), P. 1998 - 2011

Published: Jan. 22, 2022

Cytogenetic diagnostics play a crucial role in risk stratification and classification of myeloid malignancies such as acute leukemia (AML) myelodysplastic syndrome (MDS), thus influencing treatment decisions. Optical genome mapping (OGM) is novel whole method for the detection cytogenetic abnormalities. Our study assessed applicability practicality OGM diagnostic tool AML MDS patients. In total, 27 patients with or underwent routine including classical karyotyping fluorescence situ hybridization (FISH) real-time PCR analysis wherever indicated well following recently established workflow. Methods were compared regarding concordance content information. 93%, was concordant to total 61 additional variants predefined gene-set could be detected. 67% samples karyotype redefined by OGM. offers approach high cytogenetics. The has potential enter gold standard widely superseding FISH. Furthermore, can serve identify genetic regions interest future research tumor biology.

Language: Английский

---

Clinical Validation and Diagnostic Utility of Optical Genome Mapping for Enhanced Cytogenomic Analysis of Hematological Neoplasms

Journal of Molecular Diagnostics, Journal Year: 2022, Volume and Issue: 24(12), P. 1279 - 1291

Published: Oct. 17, 2022

The current standard-of-care cytogenetic techniques for the analysis of hematological malignancies include karyotyping, fluorescence in situ hybridization, and chromosomal microarray, which are labor intensive time cost prohibitive, they often do not reveal genetic complexity tumor, demonstrating need alternative technology better characterization these tumors. Herein, we report results from our clinical validation study demonstrate utility optical genome mapping (OGM), evaluated using 92 sample runs (including replicates) that included 69 well-characterized unique samples (59 neoplasms 10 controls). technical performance (quality control metrics) resulted 100% first-pass rate, with analytical (concordance) showing a sensitivity 98.7%, specificity 100%, an accuracy 99.2%. OGM demonstrated robust technical, performance, interrun, intrarun, interinstrument reproducibility. limit detection was determined to be at 5% allele fraction aneuploidy, translocation, interstitial deletion, duplication. identified several additional structural variations, revealing genomic architecture provides opportunity tumor classification, prognostication, risk stratification, therapy selection. Overall, has outperformed tests this its potential as first-tier cytogenomic test hematologic malignancies. World Health Organization classifies into myeloid lymphoid subtypes, defined by presence specific abnormalities.1Hasserjian R.P. Le Beau M.M. List A.F. Thiele J. WHO Classification Tumours Haematopoietic Lymphoid Tissues.ed 4. IARC, Lyon, France2017Google Scholar diagnostic workup routine use includes both molecular investigate single-nucleotide variants, small insertions deletions, variations (SVs).2Rack K.A. van den Berg E. Haferlach C. Beverloo H.B. Costa D. Espinet B. Foot N. Jeffries S. Martin K. O'Connor Schoumans Talley P. Telford Stioui Zemanova Z. Hastings R.J. European recommendations quality assurance haematological neoplasms.Leukemia. 2019; 33: 1851-1867Crossref PubMed Scopus (79) Google Scholar, 3Tallman M.S. Wang E.S. Altman J.K. Appelbaum F.R. Bhatt V.R. Bixby Coutre S.E. De Lima M. Fathi A.T. Fiorella Foran J.M. Hall A.C. Jacoby Lancet LeBlanc T.W. Mannis G. Marcucci M.G. Mims A. O'Donnell M.R. Olin R. Peker Perl Pollyea D.A. Pratz Prebet T. Ravandi F. Shami P.J. Stone R.M. Strickland S.A. Wieduwilt Gregory K.M. .O.C.N. Hammond L. Ogba Acute leukemia, version 3.2019, NCCN practice guidelines oncology.J Natl Compr Canc Netw. 17: 721-749Crossref (295) 4Döhner H. Estey Grimwade Amadori Büchner Dombret Ebert B.L. Fenaux Larson R.A. Levine R.L. Lo-Coco Naoe Niederwieser Ossenkoppele G.J. Sanz Sierra Tallman Tien H.F. Wei A.H. Löwenberg Diagnosis management AML adults: 2017 ELN international expert panel.Blood. 2017; 129: 424-447Crossref (3838) 5Hallek Cheson B.D. Catovsky Caligaris-Cappio Dighiero Döhner Hillmen Keating Montserrat Chiorazzi Stilgenbauer Rai K.R. Byrd J.C. Eichhorst O'Brien Robak Seymour J.F. Kipps T.J. iwCLL diagnosis, indications treatment, response assessment, supportive CLL.Blood. 2018; 131: 2745-2760Crossref (925) 6Sonneveld Avet-Loiseau Lonial Usmani Siegel Anderson K.C. Chng W.J. Moreau Attal Kyle Caers Hillengass San Miguel de Donk N.W. Einsele Bladé Durie B.G. Goldschmidt Mateos M.V. Palumbo Orlowski Treatment multiple myeloma high-risk cytogenetics: consensus International Myeloma Working Group.Blood. 2016; 127: 2955-2962Crossref (616) 7Aguilera-Diaz Vazquez I. Ariceta Mañú Blasco-Iturri Palomino-Echeverría Larrayoz M.J. García-Sanz Prieto-Conde M.I. del Carmen Chillón Alfonso-Pierola Assessment four NGS panels malignancies: suggestions panel choice or design.PLoS One. 2020; 15: e0227986Crossref (27) In past decade, significant progress been made profiling tumors next-generation sequencing technology, replaced single-variant/gene gene even whole-exome sequencing.8Sahajpal N.S. Mondal A.K. Ananth Njau Ahluwalia Jones Okechukwu Savage N.M. Kota V. Rojiani A.M. Kolhe Clinical comprehensive DNA simultaneous TMB MSI neoplasms.PLoS e0240976Crossref (7) Scholar,9Hansen M.C. Nyvold C.G. A decade whole exome haematology.Br J Haematol. 188: 367-382Crossref (21) However, recurrent abnormalities used many assist prognosis, selection, recommended professional guidelines.3Tallman Scholar,10Mikhail F.M. Heerema N.A. Rao K.W. Burnside R.D. Cherry Cooley L.D. Section E6.1- 6.4 ACMG standards guidelines: chromosome studies neoplastic blood bone marrow-acquired abnormalities.Genet Med. 18: 635-642Abstract Full Text PDF (20) currently relies on combination traditional techniques, low resolution (karyotyping), targeted, require prior knowledge [fluorescence hybridization (FISH)], cannot detect balanced SVs orientation duplicated segments (chromosomal microarrays). As result, clinically relevant information remains intractable (SOC) techniques. First, although frequently harbor acquired translocations,11Aplan P.D. Causes oncogenic translocation.Trends Genet. 2006; 22: 46-55Abstract (147) Scholar,12Wang Y. Wu Liu Jin Recurrent fusion genes leukemia: attractive target diagnosis treatment.Curr Genom. 1087-1094Crossref (29) discovery new fusions possible because lack gene-level karyotyping. Second, location insertion submicroscopic duplications remain beyond purview technologies, might result incorrect interpretation observed SV. Third, able resolve complex rearrangements structure add information. Considering limitations analysis, there can all classes higher single assay. whole-genome complete solution recently tested, but is met bioinformatics sophisticated instrumentation, remained limited (selected translocations) karyotype-level copy number (CNVs) (>5-megabase resolution); it offers benefits over conventional methods.13Duncavage E.J. Schroeder O'Laughlin Wilson MacMillan Bohannon Kruchowski Garza Du Hughes A.E.O. Robinson Heath Baty J.D. Neidich Christopher M.A. Uy G.L. Fulton R.S. Miller C.A. Payton J.E. Link D.C. Walter Westervelt DiPersio Ley Spencer D.H. Genome cancers.N Engl 2021; 384: 924-935Crossref (119) Optical (OGM) emerged than SOC Recently, gained enormous traction settings, including prenatal settings,14Sahajpal Barseghyan Hastie Chaubey tool analyses.Genes (Basel). 12: 398Crossref (39) postnatal settings,15Mantere Neveling Pebrel-Richard Benoist der Zande Kater-Baats Baatout Beek Yammine Oorsprong Hsoumi Olde-Weghuis Majdali W. Vermeulen Pauper Lebbar Stevens-Kroef Sanlaville Dupont Smeets Hoischen Schluth-Bolard El Khattabi enables constitutional aberration detection.Am Hum 108: 1409-1422Abstract (68) neoplasms,16Neveling Mantere Weghuis D.O. M.J.P.L. Next-generation assessment 52 malignancy genomes mapping.Am 1423-1435Abstract (52) solid tumors,17Goldrich D.Y. LaBarge Chartrand Zhang Sadowski Pham Way Lai C.J. Pang A.W.C. Clifford A.R. Oldakowski Goldenberg Broach J.R. Identification somatic variants mapping.J Pers 11: 142Crossref (14) concordance analysis. literature lacks any studies, critical evaluation implementation. study, (in Laboratory Improvement Amendments setting) comparison methods (karyotyping FISH), well platform This retrospective analyses replicates), representing were received laboratory karyotyping and/or FISH testing. These composed 59 adult acute leukemia (AML; n = 18), chronic lymphocytic (CLL; 15), myelodysplastic syndrome (MDS; 12), plasma cell (n 6), lymphoma 3), myeloproliferative disorders/myeloproliferative 2). addition, morphologically normal cytogenetically negative also analyzed evaluate true-negative/false-positive rates calculate metrics (Figure 1A). data blinded manner analyst (N.S.S.), then compared board-certified director (R.K.). concordant grouped under calls, other reported considered findings. marrow aspirate 45), peripheral 16), CD-138 isolated cells 5), lymph node–single-cell suspensions processed technologist previous 1B). Of samples, 64 stored –80°C within 4 days after collection (as manufacturer), whereas 6 8 had elapsed 3 18 20 2 1C). performed Institutional Review Board A: BIOMEDICAL I (Institutional registration 00000150), Augusta University 611298). On basis approval, consent waived; protected health removed, anonymized before accessing study. Ultra-high-molecular-weight isolated, labeled, Bionano Genomics Saphyr following manufacturer's protocols (Bionano Inc., Diego, CA). Briefly, frozen aliquot (650 μL) thawed, counted HemoCue (HemoCue Holding AB, Ängelholm, Sweden). Subsequently, approximately 1.5 million nucleated white centrifuged, digested proteinase K lysed Lysis Binding Buffer. precipitated nanobind magnetic disk isopropanol washed buffers (buffers B). ultra-high-molecular-weight–bound suspended elution buffer quantified Qubit broad-range double-stranded assay kits (ThermoFisher Scientific, Francisco, labeled Inc.) 750 ng purified ultra-high-molecular-weight sequence-specific motif direct labelling (DL)-green fluorophores Direct Labeling Enzyme 1 reactions. Following labeling reaction, enzyme DL-green removed two steps adsorption membrane microtiter plate. Finally, backbone stained blue stain high-sensitivity kits. Labeled loaded onto flow chips imaging. fluorescently molecules imaged instrument electrophoretically linearized nanochannel arrays. Analytical (QC) targets set achieve >400× effective coverage (>200× deemed analyzable), >70% 13 17 label density (labels per 100 kbp), >230 kbp N50 (of >150 kbp). rare variant pipeline Access 1.6 1.5/Bionano Solve 3.6 3.5 software samples. given directly aligned GRCh38, reference human assembly, (insertions, duplications, inversions, detected differences alignment labels between assembly. coverage-based algorithm enabled large CNVs aneuploidies. generated annotated known canonical sets extracted For filtered criteria following: i) confidence scores applied: insertion, 0; inversion, 0.01; duplication, –1; number, 0.99 (low stringency, filter 0). ii) GRCh38 SV mask hides difficult-to-map regions turned off iii) To narrow analyzed, out polymorphic [ie, those appeared >1% internal database > 300)]. iv) impacting gene/loci listed National Comprehensive Cancer Network/National Service/World (https://www.nccn.org/guidelines/recently-published-guidelines, https://www.england.nhs.uk/publication/national-genomic-test-directories, last accessed March 17, 2022) investigated customized bed file.18Arber Orazi Hasserjian Borowitz Bloomfield C.D. Cazzola Vardiman J.W. 2016 revision classification leukemia.Blood. 2391-2405Crossref (6518) v) Translocation, CNV >500 kb finding. Five positive percentage agreement, predictive value, evaluated. evaluation. Differences size breakpoint anticipated, methods, thus, if slightly different. centromeric breakpoints, frequency <5%, excluded (beyond capabilities iteration 400× coverage). each reportable SVs, findings (Supplemental Table S1). Although detailed investigation confirmation scope article, have provided Supplemental S1 future discoveries consider likely true events, consistent reports.16Neveling Scholar,17Goldrich neoplasms, 48 testing FISH, only 1D). cases, 14 classified cases (four more aberrations) 45 simple (fewer aberrations). total 164 aberrations reported. They 60 aneuploidies, 34 28 translocations, 11 duplications/amplifications, 16 insertions/additional material 12 marker chromosomes, ring chromosome, isochromosome, 1E). reproducibility performing comparisons. interrun comparisons, three run triplicates separate different instruments. intrarun same chip instrument. measured (QC (clinically variant) performance. (LoD) parameters (400× coverage, pipeline, threshold) assessed LoD class diluting (reported method) wild-type provide fractions: 25%, 16.6%, 12.5%, 10%, 5%. fractions (theoretical range) confirm LoD. All passed metrics, neoplasm achieved average (>150 kb) 303 (±35), map rate 87.5% (±7.5%), 15.8/100 (±1.0), 391× (±89) S2). total, 86,306 1462 sample. 4226 filtration applied (94.9% out), 71 further interrogated S3). identifying 162 mosaic loss Y <10% (4/20 3/20 cells). Because cultures cause bias clonal proportion, bulk (preculture) may below OGM. well-known neoplasms. such, aneuploidies 33 monosomies, 21 trisomies, loss-of-sex most common monosomies 5 7 trisomies 9 5) chromosome. one case CLL) correctly called 57 manually interpreted visualization viewer (the could them lower threshold). 12, –13, near threshold (5% fraction) 3/20) respectively. deletions ranged 905 up entire data. translocations balanced, unbalanced, three-way lead reoccurring fusions: RUNX1::RUNX1T1 KMT2A::ELL 1), BCR::ABL1 FGFR1::BCR 1) Furthermore, identify material/insertions 15 identity markers uncharacterized 3).Figure 3Optical resolves karyotype hybridization. circos plot summarizing (SVs) genome: 3q, t (3; 19), 5q, gain 7, 13q, rearrangement chromosomes 20. B: browser view 16: maps pter qter, C: Circos 20: intertranslocations intratranslocations chromosomes. D: gains loss, chromosome.View Large Image Figure ViewerDownload Hi-res image Download (PPT) simple, 35 least aberration, aberrations, previously corrected interpretations due cases: Case 1: (performed aspirate), cells) copies 1q CKS1B (43/50 cells), monosomy (47/50 gain/rearrangement 4p FGFR3 (23/50 confirmed 1q21.1qter (144092961_248943333)x3, (13)x1, did gene. der(4)t(4;5) (p16.3;p13.3) (1910123;32591078), 4p16.3 overlaps region dual-fusion probes detecting gain/rearrangement. translocation disrupt 4, B ). 2: CLL, 46,XY,der (4)t (4; 7) (p14; q11.2),del (11) (q22q23), dic(21;21) (q22;p11.2)12Wang Scholar/46,XY,8Sahajpal deletion 11q (ATM). (p15.1; q21.11) (2986

Language: Английский

---

The Genetics of Intellectual Disability

Brain Sciences, Journal Year: 2023, Volume and Issue: 13(2), P. 231 - 231

Published: Jan. 30, 2023

Intellectual disability (ID) has a prevalence of ~2–3% in the general population, having large societal impact. The underlying cause ID is largely genetic origin; however, identifying this past often led to long diagnostic Odysseys. Over decades, improvements technologies and strategies have these causes being more detectable: from cytogenetic analysis 1959, we moved first decade 21st century genomic microarrays with yield ~20% next-generation sequencing platforms up 60%. In review, discuss various developments, as well their associated challenges implications for field ID, which highlight revolutionizing shift clinical practice phenotype-first into genotype-first approach.

Language: Английский

---