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Bugga P, Asthana V, Drezek R. Simulation-guided tunable DNA probe design for mismatch tolerant hybridization. PLoS One 2024; 19:e0305002. [PMID: 39172820 PMCID: PMC11340886 DOI: 10.1371/journal.pone.0305002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/21/2024] [Indexed: 08/24/2024] Open
Abstract
The ability to both sensitively and specifically assess the sequence composition of a nucleic acid strand is an ever-growing field. Designing a detection scheme that can perform this function when the sequence of the target being detected deviates significantly from the canonical sequence however is difficult in part because probe/primer design is based on established Watson-Crick base-pairing rules. We present here a robust and tunable toehold-based exchange probe that can detect a sequence with a variable number of SNPs of unknown identity by inserting a series of controlled, sequential mismatches into the protector seal of the toehold probe, in an effort to make the protector seal "sloppy". We show that the mismatch-tolerant system follows predicted behavior closely even with targets containing up to four mismatches that thermodynamically deviate from the canonical sequence by up to 15 kcal/mole. The system also performs faithfully regardless of the global mismatch position on either the protector seal or target. Lastly, we demonstrate the generalizability of the approach by testing the increasingly mismatch-tolerant protectors on HIV clinical samples to show that the system is capable of resolving multiple, iteratively mutated sequences derived from numerous HIV sub-populations with remarkable precision.
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Affiliation(s)
- Pallavi Bugga
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Vishwaratn Asthana
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Rebekah Drezek
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
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2
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Zhang W, Kang Y, Cheng X, Wen J, Zhang H, Torres-Jerez I, Krom N, Udvardi MK, Scheible WR, Zhao PX. Distinguishing HapMap Accessions Through Recursive Set Partitioning in Hierarchical Decision Trees. FRONTIERS IN PLANT SCIENCE 2021; 12:628421. [PMID: 33613609 PMCID: PMC7886675 DOI: 10.3389/fpls.2021.628421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
The HapMap (haplotype map) projects have produced valuable genetic resources in life science research communities, allowing researchers to investigate sequence variations and conduct genome-wide association study (GWAS) analyses. A typical HapMap project may require sequencing hundreds, even thousands, of individual lines or accessions within a species. Due to limitations in current sequencing technology, the genotype values for some accessions cannot be clearly called. Additionally, allelic heterozygosity can be very high in some lines, causing genetic and sometimes phenotypic segregation in their descendants. Genetic and phenotypic segregation degrades the original accession's specificity and makes it difficult to distinguish one accession from another. Therefore, it is vitally important to determine and validate HapMap accessions before one conducts a GWAS analysis. However, to the best of our knowledge, there are no prior methodologies or tools that can readily distinguish or validate multiple accessions in a HapMap population. We devised a bioinformatics approach to distinguish multiple HapMap accessions using only a minimum number of genetic markers. First, we assign each candidate marker with a distinguishing score (DS), which measures its capability in distinguishing accessions. The DS score prioritizes those markers with higher percentages of homozygous genotypes (allele combinations), as they can be stably passed on to offspring. Next, we apply the "set-partitioning" concept to select optimal markers by recursively partitioning accession sets. Subsequently, we build a hierarchical decision tree in which a specific path represents the selected markers and the homogenous genotypes that can be used to distinguish one accession from others in the HapMap population. Based on these algorithms, we developed a web tool named MAD-HiDTree (Multiple Accession Distinguishment-Hierarchical Decision Tree), designed to analyze a user-input genotype matrix and construct a hierarchical decision tree. Using genetic marker data extracted from the Medicago truncatula HapMap population, we successfully constructed hierarchical decision trees by which the original 262 M. truncatula accessions could be efficiently distinguished. PCR experiments verified our proposed method, confirming that MAD-HiDTree can be used for the identification of a specific accession. MAD-HiDTree was developed in C/C++ in Linux. Both the source code and test data are publicly available at https://bioinfo.noble.org/MAD-HiDTree/.
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3
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Chiu CG, Nakamura Y, Chong KK, Huang SK, Kawas NP, Triche T, Elashoff D, Kiyohara E, Irie RF, Morton DL, Hoon DSB. Genome-wide characterization of circulating tumor cells identifies novel prognostic genomic alterations in systemic melanoma metastasis. Clin Chem 2014; 60:873-85. [PMID: 24718909 DOI: 10.1373/clinchem.2013.213611] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Circulating tumor cells (CTC) have been found in patients with metastatic melanoma and are associated with advanced melanoma stage and poor patient outcome. We hypothesize that CTC harbor genomic changes critical in the development of distant systemic metastasis. Here, we present the first genome-wide copy-number aberration (CNA) and loss of heterozygosity (LOH)-based characterization of melanoma CTC. METHODS CTC were isolated from peripheral blood monocytes of 13 melanoma patients with regional metastasis stage IIIB/C using antibodies against melanoma-associated cell surface gangliosides. RESULTS We characterized 251 CNA in CTC. Comparative analysis demonstrated >90% concordance in single-nucleotide polymorphism profiles between paired CTC and tumor metastases. In particular, there were notable recurring CNA across patients. In exploratory studies, the presence of several top CTC-associated CNA was verified in distant metastasis (stage IV) from 27 patients, suggesting that certain genomic changes are propagated from regional metastasis to CTC and to distant systemic metastases. Lastly, an exploratory biomarker panel derived from 5 CTC-associated CNA [CSMD2 (CUB and Sushi multiple domains 2), 1p35.1; CNTNAP5 (contactin associated protein-like 5), 2q14.3; NRDE2 (NRDE-2, necessary for RNA interference, domain containing), 14q32.11; ADAM6 (ADAM metallopeptidase domain 6, pseudogene), 14q32.33; and TRPM2 (transient receptor potential cation channel, subfamily m, member 2), 21q22.3] conferred prognostic utility for melanoma recurrence [hazard ratio (HR), 1.14; CI, 1.00-1.44; P = 0.0471] and death (HR, 2.86; CI, 1.23-14.42; P = 0.0014) in 35 patients with stage IIIB/C melanoma, with a 5-year disease-free survival of 13% vs 69% (P = 0.0006) and overall survival of 28% vs 94% between high-risk and low-risk groups defined by the biomarker panel, respectively. CONCLUSIONS This study provides the first detailed CNA-based profile of melanoma CTC and illustrates how CTC may be used as a novel approach for identification of systemic metastasis.
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Affiliation(s)
- Connie G Chiu
- Department of Molecular Oncology and Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, CA
| | | | | | | | | | - Timothy Triche
- Center for Personalized Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - David Elashoff
- Department of Medicine Statistics Core, UCLA School of Medicine, Los Angeles, CA
| | | | - Reiko F Irie
- Department of Biotechnology, John Wayne Cancer Institute, Santa Monica, CA
| | - Donald L Morton
- Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, CA
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4
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Slimak MA, Ables JL, Frahm S, Antolin-Fontes B, Santos-Torres J, Moretti M, Gotti C, Ibañez-Tallon I. Habenular expression of rare missense variants of the β4 nicotinic receptor subunit alters nicotine consumption. Front Hum Neurosci 2014; 8:12. [PMID: 24478678 PMCID: PMC3902282 DOI: 10.3389/fnhum.2014.00012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/07/2014] [Indexed: 01/23/2023] Open
Abstract
The CHRNA5-CHRNA3-CHRNB4 gene cluster, encoding the α5, α3, and β4 nicotinic acetylcholine receptor (nAChR) subunits, has been linked to nicotine dependence. The habenulo-interpeduncular (Hb-IPN) tract is particularly enriched in α3β4 nAChRs. We recently showed that modulation of these receptors in the medial habenula (MHb) in mice altered nicotine consumption. Given that β4 is rate-limiting for receptor activity and that single nucleotide polymorphisms (SNPs) in CHRNB4 have been linked to altered risk of nicotine dependence in humans, we were interested in determining the contribution of allelic variants of β4 to nicotine receptor activity in the MHb. We screened for missense SNPs that had allele frequencies >0.0005 and introduced the corresponding substitutions in Chrnb4. Fourteen variants were analyzed by co-expression with α3. We found that β4A90I and β4T374I variants, previously shown to associate with reduced risk of smoking, and an additional variant β4D447Y, significantly increased nicotine-evoked current amplitudes, while β4R348C, the mutation most frequently encountered in sporadic amyotrophic lateral sclerosis (sALS), showed reduced nicotine currents. We employed lentiviruses to express β4 or β4 variants in the MHb. Immunoprecipitation studies confirmed that β4 lentiviral-mediated expression leads to specific upregulation of α3β4 but not β2 nAChRs in the Mhb. Mice injected with the β4-containing virus showed pronounced aversion to nicotine as previously observed in transgenic Tabac mice overexpressing Chrnb4 at endogenous sites including the MHb. Habenular expression of the β4 gain-of-function allele T374I also resulted in strong aversion, while transduction with the β4 loss-of function allele R348C failed to induce nicotine aversion. Altogether, these data confirm the critical role of habenular β4 in nicotine consumption, and identify specific SNPs in CHRNB4 that modify nicotine-elicited currents and alter nicotine consumption in mice.
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Affiliation(s)
- Marta A Slimak
- Molecular Neurobiology Group, Max Delbrück Center for Molecular Medicine Berlin, Germany
| | - Jessica L Ables
- Laboratory of Molecular Biology, The Rockefeller University New York, NY, USA
| | - Silke Frahm
- Molecular Neurobiology Group, Max Delbrück Center for Molecular Medicine Berlin, Germany
| | - Beatriz Antolin-Fontes
- Molecular Neurobiology Group, Max Delbrück Center for Molecular Medicine Berlin, Germany ; Laboratory of Molecular Biology, The Rockefeller University New York, NY, USA
| | - Julio Santos-Torres
- Molecular Neurobiology Group, Max Delbrück Center for Molecular Medicine Berlin, Germany
| | - Milena Moretti
- Consiglio Nazionale delle Ricerche Institute of Neuroscience and Biometra Department, University of Milan Milan, Italy
| | - Cecilia Gotti
- Consiglio Nazionale delle Ricerche Institute of Neuroscience and Biometra Department, University of Milan Milan, Italy
| | - Inés Ibañez-Tallon
- Molecular Neurobiology Group, Max Delbrück Center for Molecular Medicine Berlin, Germany ; Laboratory of Molecular Biology, The Rockefeller University New York, NY, USA
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5
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Affiliation(s)
- Joanne Mason
- West Midlands Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, Edgbaston, Birmingham, B15 2TG, UK
| | - Michael Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, Edgbaston, Birmingham, B15 2TG, UK
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6
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Li X, Galipeau PC, Paulson TG, Sanchez CA, Arnaudo J, Liu K, Sather CL, Kostadinov RL, Odze RD, Kuhner MK, Maley CC, Self SG, Vaughan TL, Blount PL, Reid BJ. Temporal and spatial evolution of somatic chromosomal alterations: a case-cohort study of Barrett's esophagus. Cancer Prev Res (Phila) 2013; 7:114-27. [PMID: 24253313 DOI: 10.1158/1940-6207.capr-13-0289] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
All cancers are believed to arise by dynamic, stochastic somatic genomic evolution with genome instability, generation of diversity, and selection of genomic alterations that underlie multistage progression to cancer. Advanced esophageal adenocarcinomas have high levels of somatic copy number alterations. Barrett's esophagus is a risk factor for developing esophageal adenocarcinoma, and somatic chromosomal alterations (SCA) are known to occur in Barrett's esophagus. The vast majority (∼95%) of individuals with Barrett's esophagus do not progress to esophageal adenocarcinoma during their lifetimes, but a small subset develop esophageal adenocarcinoma, many of which arise rapidly even in carefully monitored patients without visible endoscopic abnormalities at the index endoscopy. Using a well-designed, longitudinal case-cohort study, we characterized SCA as assessed by single-nucleotide polymorphism arrays over space and time in 79 "progressors" with Barrett's esophagus as they approach the diagnosis of cancer and 169 "nonprogressors" with Barrett's esophagus who did not progress to esophageal adenocarcinoma over more than 20,425 person-months of follow-up. The genomes of nonprogressors typically had small localized deletions involving fragile sites and 9p loss/copy neutral LOH that generate little genetic diversity and remained relatively stable over prolonged follow-up. As progressors approach the diagnosis of cancer, their genomes developed chromosome instability with initial gains and losses, genomic diversity, and selection of SCAs followed by catastrophic genome doublings. Our results support a model of differential disease dynamics in which nonprogressor genomes largely remain stable over prolonged periods, whereas progressor genomes evolve significantly increased SCA and diversity within four years of esophageal adenocarcinoma diagnosis, suggesting a window of opportunity for early detection.
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Affiliation(s)
- Xiaohong Li
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024.
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7
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Markello TC, Han T, Carlson-Donohoe H, Ahaghotu C, Harper U, Jones M, Chandrasekharappa S, Anikster Y, Adams DR, Gahl WA, Boerkoel CF. Recombination mapping using Boolean logic and high-density SNP genotyping for exome sequence filtering. Mol Genet Metab 2012; 105:382-9. [PMID: 22264778 PMCID: PMC3515651 DOI: 10.1016/j.ymgme.2011.12.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 12/19/2011] [Indexed: 11/28/2022]
Abstract
Whole genome sequence data for small pedigrees has been shown to provide sufficient information to resolve detailed haplotypes in small pedigrees. Using such information, recombinations can be mapped onto chromosomes, compared with the segregation of a disease of interest and used to filter genome sequence variants. We now show that relatively inexpensive SNP array data from small pedigrees can be used in a similar manner to provide a means of identifying regions of interest in exome sequencing projects. We demonstrate that in those situations where one can assume complete penetrance and parental DNA is available, SNP recombination mapping using Boolean logic identifies chromosomal regions identical to those detected by multipoint linkage using microsatellites but with much less computation. We further show that this approach is successful because the probability of a double crossover between informative SNP loci is negligible. Our observations provide a rationale for using SNP arrays and recombination mapping as a rapid and cost-effective means of incorporating chromosome segregation information into exome sequencing projects intended for disease-gene identification.
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Affiliation(s)
- Thomas C Markello
- National Human Genome Research Institute, NIH, Bethesda, MD 20892-1611, USA.
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8
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van der Veken LT, Buijs A. Array CGH in human leukemia: from somatics to genetics. Cytogenet Genome Res 2011; 135:260-70. [PMID: 21893961 DOI: 10.1159/000330629] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During the past decade, array CGH has been applied to study copy number alterations in the genome in human leukemia in relation to prediction of prognosis or responsiveness to therapy. In the first segment of this review, we will focus on the identification of acquired mutations by array CGH, followed by studies on the pathogenesis of leukemia associated with germline genetic variants, phenotypic presentation and response to treatment. In the last section, we will discuss constitutional genomic aberrations causally related to myeloid leukemogenesis.
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Affiliation(s)
- L T van der Veken
- Section of Genome Diagnostics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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9
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Wirapati P, Forner K, Delgado-Vega A, Alarcón-Riquelme M, Delorenzi M, Wojcik J. Detecting epistasis with restricted response patterns in pairs of biallelic loci. Ann Hum Genet 2010; 75:133-45. [PMID: 21118193 DOI: 10.1111/j.1469-1809.2010.00625.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Well-established examples of genetic epistasis between a pair of loci typically show characteristic patterns of phenotypic distributions in joint genotype tables. However, inferring epistasis given such data is difficult due to the lack of power in commonly used approaches, which decompose the epistatic patterns into main plus interaction effects followed by testing the interaction term. Testing additive-only or all terms may have more power, but they are sensitive to nonepistatic patterns. Alternatively, the epistatic patterns of interest can be enumerated and the best matching one is found by searching through the possibilities. Although this approach requires multiple testing correction over possible patterns, each pattern can be fitted with a regression model with just one degree of freedom and thus the overall power can still be high, if the number of possible patterns is limited. Here we compare the power of the linear decomposition and pattern search methods, by applying them to simulated data generated under several patterns of joint genotype effects with simple biological interpretations. Interaction-only tests are the least powerful; while pattern search approach is the most powerful if the range of possibilities is restricted, but still includes the true pattern.
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10
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Abstract
Single nucleotide polymorphism arrays (SNP-A) have recently been widely applied as a powerful karyotyping tool in numerous translational cancer studies. SNP-A complements traditional metaphase cytogenetics with the unique ability to delineate a previously hidden chromosomal defect, copy neutral loss of heterozygosity (CN-LOH). Emerging data demonstrate that selected hematologic malignancies exhibit abundant CN-LOH, often in the setting of a normal metaphase karyotype and no previously identified clonal marker. In this review, we explore emerging biologic and clinical features of CN-LOH relevant to hematologic malignancies. In myeloid malignancies, CN-LOH has been associated with the duplication of oncogenic mutations with concomitant loss of the normal allele. Examples include JAK2, MPL, c-KIT, and FLT3. More recent investigations have focused on evaluation of candidate genes contained in common CN-LOH and deletion regions and have led to the discovery of tumor suppressor genes, including c-CBL and family members, as well as TET2. Investigations into the underlying mechanisms generating CN-LOH have great promise for elucidating general cancer mechanisms. We anticipate that further detailed characterization of CN-LOH lesions will probably facilitate our discovery of a more complete set of pathogenic molecular lesions, disease and prognosis markers, and better understanding of the initiation and progression of hematologic malignancies.
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Kissel HD, Galipeau PC, Li X, Reid BJ. Translation of an STR-based biomarker into a clinically compatible SNP-based platform for loss of heterozygosity. Cancer Biomark 2009; 5:143-58. [PMID: 19407369 DOI: 10.3233/cbm-2009-0618] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Loss of heterozygosity (LOH) has been shown to be a promising biomarker of cancer risk in patients with premalignant conditions. In this study we describe analytical validation in clinical biopsy samples of a SNP-based pyrosequencing panel targeting regions of LOH on chromosomes 17p and 9p including TP53 and CDKN2A tumor suppressor genes. Assays were tested for analytic specificity, sensitivity, efficiency, and reproducibility. Accuracy was evaluated by comparing SNP-based LOH results to those obtained by previously well-studied short tandem repeat polymorphisms (STRs) in DNA derived from different tissue sources including fresh-frozen endoscopic biopsies, samples from surgical resections, and formalin-fixed paraffin-embedded sections. A 17p/9p LOH panel comprised of 43 SNPs was designed to amplify with universal assay conditions in a two-step PCR and sequence-by-synthesis reaction that can be completed in two hours and 10 minutes. The methods presented can be a model for developing a SNP-based LOH approach targeted to any chromosomal region of interest for other premalignant conditions and this panel could be incorporated as part of a biomarker for cancer risk prediction, early detection, or as entry criteria for randomized trials.
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Affiliation(s)
- Heather D Kissel
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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12
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Maciejewski JP, Tiu RV, O'Keefe C. Application of array-based whole genome scanning technologies as a cytogenetic tool in haematological malignancies. Br J Haematol 2009; 146:479-88. [PMID: 19563474 DOI: 10.1111/j.1365-2141.2009.07757.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Karyotypic analysis provides useful diagnostic information in many haematological malignancies. However, standard metaphase cytogenetics has technical limitations that result in the underestimation of the degree of chromosomal changes. Array-based technologies can be used for karyotyping and can supplant some of the shortcomings of metaphase cytogenetics, and include single nucleotide polymorphism arrays (SNP-A) and comparative genomic hybridization arrays (CGH-A). Array-based cytogenetic tools do not rely on cell division, have superb resolution for unbalanced lesions and allow for the detection of copy number-neutral loss of heterozygosity, a type of lesion not seen with metaphase cytogenetics. Moreover, genomic array analysis is automated and results can be objectively and systematically analysed using biostatistical algorithms. As a potential advantage over genomic approaches, metaphase cytogenetics can detect balanced chromosomal defects and resolves clonal mosaicism. Initial studies performed in various haematological malignancies indicate the potential of SNP-A-based karyotyping as a useful clinical cytogenetic detection tool. The current effort is aimed at developing rational diagnostic algorithms for the detection of somatic defects and the establishment of clinical correlations for novel SNP-A-detected chromosomal defects, including acquired somatic uniparental disomy. SNP-A can complement metaphase karyotyping and will probably play an important role in clinical cytogenetic diagnostics.
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Affiliation(s)
- Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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13
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Hanlon K, Ellard S, Rudin CE, Thorne S, Davies T, Harries LW. Evaluation of 13q14 status in patients with chronic lymphocytic leukemia using single nucleotide polymorphism-based techniques. J Mol Diagn 2009; 11:298-305. [PMID: 19460942 DOI: 10.2353/jmoldx.2009.080167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deletions of chromosome 13q14 are common in chronic lymphocytic leukemia and other cancers, demonstrating the importance of this region in tumorigenesis. We report the use of two single-nucleotide polymorphism (SNP)-based techniques to determine 13q loss of heterozygosity (LOH) status in 15 patients with CLL: (i) digital SNP (dSNP), where analysis of heterozygous SNPs detects allelic imbalances, and (ii) DNA sequencing, where LOH is identified by comparison of allelic peak heights in normal and neoplastic cells. The SNP-based techniques were compared with established molecular techniques, fluorescence in situ hybridization and multiplex ligation-dependent probe amplification, to determine their utility and relative sensitivity. dSNP proved to be the most sensitive technique, identifying 13q14 LOH in 11 of 13 (85%) patients (95% CI: 55%, 98%) without the need for neoplastic cell enrichment. Three cases showed evidence of LOH by dSNP that was not apparent by other techniques. In 8 of 13 (62%) cases, partial or interstitial patterns of LOH were observed by dSNP. Our findings demonstrate that dSNP represents a useful, sensitive technique for the analysis of chromosomal aberrations that result in LOH. It may have applications for the analysis of other malignancies that are difficult to assess by conventional molecular techniques.
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Affiliation(s)
- Katy Hanlon
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
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14
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Loss of heterozygosity 4q24 and TET2 mutations associated with myelodysplastic/myeloproliferative neoplasms. Blood 2009; 113:6403-10. [PMID: 19372255 DOI: 10.1182/blood-2009-02-205690] [Citation(s) in RCA: 307] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chromosomal abnormalities are frequent in myeloid malignancies, but in most cases of myelodysplasia (MDS) and myeloproliferative neoplasms (MPN), underlying pathogenic molecular lesions are unknown. We identified recurrent areas of somatic copy number-neutral loss of heterozygosity (LOH) and deletions of chromosome 4q24 in a large cohort of patients with myeloid malignancies including MDS and related mixed MDS/MPN syndromes using single nucleotide polymorphism arrays. We then investigated genes in the commonly affected area for mutations. When we sequenced TET2, we found homozygous and hemizygous mutations. Heterozygous and compound heterozygous mutations were found in patients with similar clinical phenotypes without LOH4q24. Clinical analysis showed most TET2 mutations were present in patients with MDS/MPN (58%), including CMML (6/17) or sAML (32%) evolved from MDS/MPN and typical MDS (10%), suggesting they may play a ubiquitous role in malignant evolution. TET2 mutations affected conserved domains and the N terminus. TET2 is widely expressed in hematopoietic cells but its function is unknown, and it lacks homology to other known genes. The frequency of mutations in this candidate myeloid regulatory gene suggests an important role in the pathogenesis of poor prognosis MDS/MPN and sAML and may act as a disease gene marker for these often cytogenetically normal disorders.
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15
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Tuna M, Knuutila S, Mills GB. Uniparental disomy in cancer. Trends Mol Med 2009; 15:120-8. [PMID: 19246245 DOI: 10.1016/j.molmed.2009.01.005] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 01/06/2009] [Accepted: 01/06/2009] [Indexed: 02/03/2023]
Abstract
Uniparental disomy (UPD) results when both copies of a chromosome pair originate from one parent. In humans, this might result in developmental disease or cancer due to either the production of homozygosity (caused by mutated or methylated genes or by microRNA sequences) or an aberrant pattern of imprinting. Constitutional UPD is associated with meiotic errors, resulting in developmental diseases, whereas acquired UPD probably occurs as a result of a mitotic error in somatic cells, which can be an important step in cancer development and progression. This review summarizes the mechanisms underlying UPD and their emerging association with cancer.
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Affiliation(s)
- Musaffe Tuna
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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16
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Li X, Galipeau PC, Sanchez CA, Blount PL, Maley CC, Arnaudo J, Peiffer DA, Pokholok D, Gunderson KL, Reid BJ. Single nucleotide polymorphism-based genome-wide chromosome copy change, loss of heterozygosity, and aneuploidy in Barrett's esophagus neoplastic progression. Cancer Prev Res (Phila) 2008; 1:413-23. [PMID: 19138988 PMCID: PMC2882787 DOI: 10.1158/1940-6207.capr-08-0121] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromosome copy gain, loss, and loss of heterozygosity (LOH) involving most chromosomes have been reported in many cancers; however, less is known about chromosome instability in premalignant conditions. 17p LOH and DNA content abnormalities have been previously reported to predict progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA). Here, we evaluated genome-wide chromosomal instability in multiple stages of BE and EA in whole biopsies. Forty-two patients were selected to represent different stages of progression from BE to EA. Whole BE or EA biopsies were minced, and aliquots were processed for flow cytometry and genotyped with a paired constitutive control for each patient using 33,423 single nucleotide polymorphisms (SNP). Copy gains, losses, and LOH increased in frequency and size between early- and late-stage BE (P < 0.001), with SNP abnormalities increasing from <2% to >30% in early and late stages, respectively. A set of statistically significant events was unique to either early or late, or both, stages, including previously reported and novel abnormalities. The total number of SNP alterations was highly correlated with DNA content aneuploidy and was sensitive and specific to identify patients with concurrent EA (empirical receiver operating characteristic area under the curve = 0.91). With the exception of 9p LOH, most copy gains, losses, and LOH detected in early stages of BE were smaller than those detected in later stages, and few chromosomal events were common in all stages of progression. Measures of chromosomal instability can be quantified in whole biopsies using SNP-based genotyping and have potential to be an integrated platform for cancer risk stratification in BE.
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Affiliation(s)
- Xiaohong Li
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle WA, 98109
| | - Patricia C. Galipeau
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle WA, 98109
| | - Carissa A. Sanchez
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle WA, 98109
| | - Patricia L. Blount
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle WA, 98109
- Department of Medicine, University of Washington, Seattle, WA, 98195
| | | | - Jessica Arnaudo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | | | | | | | - Brian J. Reid
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle WA, 98109
- Department of Medicine, University of Washington, Seattle, WA, 98195
- Genome Sciences, University of Washington, Seattle, WA, 98195
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Abstract
Over the years, methods of cytogenetic analysis evolved and became part of routine laboratory testing, providing valuable diagnostic and prognostic information in hematologic disorders. Karyotypic aberrations contribute to the understanding of the molecular pathogenesis of disease and thereby to rational application of therapeutic modalities. Most of the progress in this field stems from the application of metaphase cytogenetics (MC), but recently, novel molecular technologies have been introduced that complement MC and overcome many of the limitations of traditional cytogenetics, including a need for cell culture. Whole genome scanning using comparative genomic hybridization and single nucleotide polymorphism arrays (CGH-A; SNP-A) can be used for analysis of somatic or clonal unbalanced chromosomal defects. In SNP-A, the combination of copy number detection and genotyping enables diagnosis of copy-neutral loss of heterozygosity, a lesion that cannot be detected using MC but may have important pathogenetic implications. Overall, whole genome scanning arrays, despite the drawback of an inability to detect balanced translocations, allow for discovery of chromosomal defects in a higher proportion of patients with hematologic malignancies. Newly detected chromosomal aberrations, including somatic uniparental disomy, may lead to more precise prognostic schemes in many diseases.
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