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1.
Nature ; 621(7977): 129-137, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37587346

ABSTRACT

Homologous recombination (HR) deficiency is associated with DNA rearrangements and cytogenetic aberrations1. Paradoxically, the types of DNA rearrangements that are specifically associated with HR-deficient cancers only minimally affect chromosomal structure2. Here, to address this apparent contradiction, we combined genome-graph analysis of short-read whole-genome sequencing (WGS) profiles across thousands of tumours with deep linked-read WGS of 46 BRCA1- or BRCA2-mutant breast cancers. These data revealed a distinct class of HR-deficiency-enriched rearrangements called reciprocal pairs. Linked-read WGS showed that reciprocal pairs with identical rearrangement orientations gave rise to one of two distinct chromosomal outcomes, distinguishable only with long-molecule data. Whereas one (cis) outcome corresponded to the copying and pasting of a small segment to a distant site, a second (trans) outcome was a quasi-balanced translocation or multi-megabase inversion with substantial (10 kb) duplications at each junction. We propose an HR-independent replication-restart repair mechanism to explain the full spectrum of reciprocal pair outcomes. Linked-read WGS also identified single-strand annealing as a repair pathway that is specific to BRCA2 deficiency in human cancers. Integrating these features in a classifier improved discrimination between BRCA1- and BRCA2-deficient genomes. In conclusion, our data reveal classes of rearrangements that are specific to BRCA1 or BRCA2 deficiency as a source of cytogenetic aberrations in HR-deficient cells.


Subject(s)
BRCA1 Protein , BRCA2 Protein , Chromosome Aberrations , DNA Repair , Neoplasms , Humans , BRCA1 Protein/deficiency , BRCA1 Protein/genetics , BRCA2 Protein/deficiency , BRCA2 Protein/genetics , Chromosome Inversion , DNA Repair/genetics , Neoplasms/genetics , Translocation, Genetic/genetics , Homologous Recombination , Cytogenetic Analysis , Chromosome Aberrations/classification
2.
Bull Exp Biol Med ; 171(3): 357-361, 2021 Jul.
Article in English | MEDLINE | ID: mdl-34297287

ABSTRACT

We studied the effect of technogenic radiation on the degree of promoter methylation in genes involved in apoptosis in blood lymphocytes of workers exposed to long-term γ-radiation during their professional activities. Blood samples for the analysis were obtained from 11 conventionally healthy men aged from 54 to 71 years (mean 66 years), workers of the Siberian Group of Chemical Enterprises working experience from 27 to 40 years (mean 30 years); the external exposure dose was 175.88 mSv (158.20-207.81 mSv). In all examined subjects, the degree of methylation of the promoters of apoptosis-related genes ranged from 0.22 to 50.00%. A correlation was found between the degree of methylation of BCLAF1 promoters (p=0.035) with the age of workers, BAX promoters (p=0.0289) with high content of aberrant cells, and APAF1 promoters (p=0.0152) with increased number of dicentric chromosomes. A relationship was found between the dose of external irradiation and the degree of methylation of gene promoters of BAD (p=0.0388), BID (р=0.0426), and HRK (р=0.0101) genes.


Subject(s)
Chromosome Aberrations/radiation effects , DNA Methylation , Epigenesis, Genetic , Lymphocytes/radiation effects , Occupational Exposure/adverse effects , Promoter Regions, Genetic , Radiation Exposure/adverse effects , Aged , Apoptosis/genetics , Apoptosis Regulatory Proteins/genetics , Apoptosis Regulatory Proteins/metabolism , Apoptotic Protease-Activating Factor 1/genetics , Apoptotic Protease-Activating Factor 1/metabolism , BH3 Interacting Domain Death Agonist Protein/genetics , BH3 Interacting Domain Death Agonist Protein/metabolism , Chromosome Aberrations/classification , Gamma Rays/adverse effects , Humans , Lymphocytes/metabolism , Lymphocytes/pathology , Male , Middle Aged , Radiometry , Repressor Proteins/genetics , Repressor Proteins/metabolism , Siberia , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism , bcl-2-Associated X Protein/genetics , bcl-2-Associated X Protein/metabolism , bcl-Associated Death Protein/genetics , bcl-Associated Death Protein/metabolism
3.
Ultrasound Obstet Gynecol ; 58(3): 377-387, 2021 Sep.
Article in English | MEDLINE | ID: mdl-33142350

ABSTRACT

OBJECTIVE: To evaluate comprehensively, using chromosomal microarray analysis (CMA) and exome sequencing (ES), the prevalence of chromosomal abnormalities and sequence variants in unselected fetuses with congenital heart defect (CHD) and to evaluate the potential diagnostic yields of CMA and ES for different CHD subgroups. METHODS: This was a study of 360 unselected singleton fetuses with CHD detected by echocardiography, referred to our department for genetic testing between February 2018 and December 2019. We performed CMA, as a routine test for aneuploidy and copy number variations (CNV), and then, in cases without aneuploidy or pathogenic CNV on CMA, we performed ES. RESULTS: Overall, positive genetic diagnoses were made in 84 (23.3%) fetuses: chromosomal abnormalities were detected by CMA in 60 (16.7%) and sequence variants were detected by ES in a further 24 (6.7%) cases. The detection rate of pathogenic and likely pathogenic genetic variants in fetuses with non-isolated CHD (32/83, 38.6%) was significantly higher than that in fetuses with isolated CHD (52/277, 18.8%) (P < 0.001), this difference being due mainly to the difference in frequency of aneuploidy between the two groups. The prevalence of a genetic defect was highest in fetuses with an atrioventricular septal defect (36.8%), ventricular septal defect with or without atrial septal defect (28.4%), conotruncal defect (22.2%) or right ventricular outflow tract obstruction (20.0%). We also identified two novel missense mutations (c.2447G>C, p.Arg816Pro; c.1171C>T, p.Arg391Cys) and a new phenotype caused by variants in PLD1. CONCLUSIONS: Chromosomal abnormalities were identified in 16.7% and sequence variants in a further 6.7% of fetuses with CHD. ES should be offered to all pregnant women with a CHD fetus without chromosomal abnormality or pathogenic CNV identified by CMA, regardless of whether the CHD is isolated. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.


Subject(s)
Exome Sequencing , Fetus/abnormalities , Heart Defects, Congenital/diagnosis , Microarray Analysis , Prenatal Diagnosis/methods , Adult , Aneuploidy , Chromosome Aberrations/classification , Chromosome Aberrations/embryology , DNA Copy Number Variations , Echocardiography , Female , Fetus/embryology , Genetic Variation , Heart Defects, Congenital/embryology , Heart Defects, Congenital/genetics , Humans , Pregnancy , Prevalence , Ultrasonography, Prenatal
4.
SEMERGEN, Soc. Esp. Med. Rural Gen. (Ed. Impr.) ; 46(5): 355-362, jul.-ago. 2020. ilus, tab
Article in Spanish | IBECS | ID: ibc-197323

ABSTRACT

La distrofia muscular miotónica tipo 1 (DM1) o enfermedad de Steinert (CIE-9-C: 359.21; CIE-10-ES: G71.11, ORPHA: 273) es una miopatía autosómica dominante de baja prevalencia (<5/10.000) con penetrancia casi completa y daño multiorgánico (neurológico, cardiológico, respiratorio, endocrinológico y digestivo). Es una de las enfermedades humanas con mayor variabilidad clínica. Los síntomas más incapacitantes o molestos para estos enfermos (limitación de la movilidad, cansancio crónico, somnolencia diurna o trastornos digestivos) y sus familias (apatía y falta de iniciativa) no son necesariamente los de peor pronóstico. Las complicaciones respiratorias y los trastornos cardíacos reducen la esperanza de vida de los afectados. No existe tratamiento que modifique su evolución. La función del médico de atención primaria es decisiva en el seguimiento de la DM1, ya sea coordinando a las diferentes especialidades implicadas en el mismo o detectando las complicaciones tratables, en las cuales se centra el presente trabajo


Myotonic dystrophy type 1 (DM1) or Steinert's disease (CIE-9-C: 359.21; CIE-10-ES: G71.11, ORPHA: 273) is a rare autosomal dominant inherited myopathy with almost complete penetrance and multisystemic consequences (neurological, cardiological, respiratory, endocrinological, and gastrointestinal). It is one of the clinical most variable diseases. The most bothersome symptoms for the patients (mobility problems, fatigue, hypersomnia, or gastrointestinal symptoms) and their families (apathy, lack of initiative) are not necessarily the most dangerous. Respiratory problems and cardiac arrhythmias shorten life expectancy. There is no specific treatment. The role of the Primary Care physician is crucial in the follow-up of DM1, either by coordinating the different professionals or detecting treatable complications. This work addresses the latter


Subject(s)
Humans , Myotonic Dystrophy/genetics , Deglutition Disorders/etiology , Myotonia Congenita/genetics , Muscle Weakness/etiology , Chromosome Aberrations/classification , Trinucleotide Repeat Expansion/genetics , Creatine Kinase/analysis , Patient Care Team/organization & administration , Heart Diseases/epidemiology , Respiration Disorders/epidemiology , Endocrine System Diseases/epidemiology
5.
Oncol Rep ; 43(3): 877-885, 2020 03.
Article in English | MEDLINE | ID: mdl-32020221

ABSTRACT

Subjectivity in oral dysplasia grading has prompted evaluation of molecular­based tests to predict malignant transformation. Aneuploidy detected by DNA image­based cytometry (ICM) is currently the best predictor but fails to detect certain high risk lesions. A novel multiplex fluorescence in situ hybridization (FISH) panel was used to explore possible explanations by detecting aneuploidy at the single cell level. FISH was compared to reference standard DNA ICM in 19 oral lesions with epithelial dysplasia and used to characterize the cellular architecture. Copy number variation at 3q28, 7p11.2, 8q24.3, 11q13.3 and 20q13.12 and matched chromosome specific loci were assessed by dual­color FISH to assess numerical and spatial patterns of copy number increase and gene amplification. FISH revealed wide variation in copy number at different loci. Only low level copy number gain was present and often in only a small proportion of cells, although usually with all or all but one locus (9/12). Four cases showed gene amplification, one at two loci. Some probes revealed an internal presumed clonal structure within lesions not apparent in routine histological examination. Both methods produced similar diagnostic results with concordance in detection of aneuploidy by both methods in 17 out of 19 samples (89%). We have shown that oral dysplastic lesions may contain very few aneuploid cells at a cellular level, high copy number gain is rare and changes appear to arise from large chromosomal fragment duplications. Single stem lines are relatively homogeneous for loci with copy number gain but there is a subclonal structure revealed by gene amplification in some lesions.


Subject(s)
Aneuploidy , Carcinoma in Situ/genetics , DNA Copy Number Variations/genetics , Mouth Neoplasms/genetics , Adult , Aged , Aged, 80 and over , Carcinoma in Situ/diagnosis , Carcinoma in Situ/pathology , Chromosome Aberrations/classification , DNA, Neoplasm/genetics , Epithelial Cells/pathology , Female , Flow Cytometry , Gene Amplification/genetics , Humans , In Situ Hybridization, Fluorescence , Male , Middle Aged , Mouth Neoplasms/diagnosis , Mouth Neoplasms/pathology
6.
J Obstet Gynaecol ; 40(4): 443-447, 2020 May.
Article in English | MEDLINE | ID: mdl-31809620

ABSTRACT

The aim of this study was to analyse the factors associated with fetal pleural effusion over the past five years in a single institute in the South of China. Between January 2011 and May 2016, 129 foetuses with pleural effusion were referred to the Fetal Medicine Unit in Guangzhou's Women and Children's Medical Center. Seventy-nine women accepted an invasive procedure to rule out chromosomal abnormalities, fetal anaemia, intrauterine infections or some of the submicroscopic chromosomal abnormalities. Our results showed that chromosomal anomalies occurred in 15.2% (12/79) of cases including 8 Turner syndrome (45, X) (10.1%), 3 trisomy 21 (3.8%) and 1 trisomy 13 (1.3%). Pathological microdeletion or microduplication syndrome occurred in 3 out of 36 (8.3%) prenatal samples with normal karyotype and structural defects. Eight foetuses (10.1%) affected with haemoglobin Bart's disease showed pleural effusion at second or third trimester. Two cases (2.5%) were found to have an intrauterine infection. In conclusion, fetal pleural effusion has a close correlation with chromosomal abnormality. CMA may increase the detection rate of chromosomal aberrations, especially for micro-deletion or micro-duplication syndromes. In the South of China, Thalassemia must be considered when a fetal pleural effusion is detected.Impact statementWhat is already known on this subject? The aetiology of fetal pleural effusion includes a chromosomal abnormality, a congenital heart disease, congenital infections and a number of genetic syndromes.What do the results of this study add? This is the first retrospective study to analyse the aetiology of fetal pleural effusion in one institute in the South of China.What are the implications of these findings for clinical practice and/or further research? Besides the chromosomal abnormality, micro-deletion and micro-duplication syndromes were also detected in our study. We feel that thalassemia must be considered when fetal pleural effusion is detected in South China.


Subject(s)
Chromosome Disorders , Fetal Diseases , Pleural Effusion , Adult , China/epidemiology , Chromosome Aberrations/classification , Chromosome Aberrations/statistics & numerical data , Chromosome Disorders/diagnosis , Chromosome Disorders/epidemiology , Factor Analysis, Statistical , Female , Fetal Diseases/diagnosis , Fetal Diseases/epidemiology , Fetal Diseases/etiology , Humans , Pleural Effusion/diagnostic imaging , Pleural Effusion/epidemiology , Pregnancy , Pregnancy Trimesters , Prenatal Diagnosis , Risk Factors , Thalassemia/epidemiology , Ultrasonography, Prenatal/methods , Ultrasonography, Prenatal/statistics & numerical data
7.
Mol Genet Genomic Med ; 8(2): e1087, 2020 02.
Article in English | MEDLINE | ID: mdl-31830383

ABSTRACT

BACKGROUND: Detection of chromosomal abnormalities is crucial in various medical areas; to diagnose birth defects, genetic disorders, and infertility, among other complex phenotypes, in individuals across a wide range of ages. Hence, the present study wants to contribute to the knowledge of type and frequency of chromosomal alterations and polymorphisms in Ecuador. METHODS: Cytogenetic registers from different Ecuadorian provinces have been merged and analyzed to construct an open-access national registry of chromosome alterations and polymorphisms. RESULTS: Of 28,806 karyotypes analyzed, 6,008 (20.9%) exhibited alterations. Down syndrome was the most frequent autosome alteration (88.28%), followed by Turner syndrome (60.50%), a gonosome aneuploidy. A recurrent high percentage of Down syndrome mosaicism (7.45%) reported here, as well as by previous Ecuadorian preliminary registries, could be associated with geographic location and admixed ancestral composition. Translocations (2.46%) and polymorphisms (7.84%) were not as numerous as autosomopathies (64.33%) and gonosomopathies (25.37%). Complementary to conventional cytogenetics tests, molecular tools have allowed identification of submicroscopic alterations regions or candidate genes which can be possibly implicated in patients' symptoms and phenotypes. CONCLUSION: The Ecuadorian National Registry of Chromosome Alterations and Polymorphisms provides a baseline to better understand chromosomal abnormalities in Ecuador and therefore their clinical management and awareness. This data will guide public policy makers to promote and financially support cytogenetic and genetic testing.


Subject(s)
Chromosome Disorders/genetics , Cytogenetic Analysis/statistics & numerical data , Genetic Testing/statistics & numerical data , Registries/statistics & numerical data , Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , Chromosome Aberrations/classification , Chromosome Disorders/classification , Chromosome Disorders/diagnosis , Chromosome Disorders/epidemiology , Databases, Genetic , Ecuador , Female , Humans , Infant , Male , Middle Aged , Phenotype , Polymorphism, Genetic
8.
Mol Genet Genomic Med ; 7(12): e980, 2019 12.
Article in English | MEDLINE | ID: mdl-31643138

ABSTRACT

BACKGROUND: Our aim was to conduct a comprehensive genetic evaluation using the combination of QF-PCR (quantitative fluorescence polymerase chain reaction) and aCGH (array comparative genomic hybridization) for the detection of the frequency and type of chromosome aberrations in recurrent miscarriage (RM) in the clinical setting. METHODS: This retrospective study was conducted on 73 first-trimester products of conception (POC) between September 2014 and February 2017. The POCs were collected from 73 women with at least one previous miscarriage and analyzed for chromosomal anomalies using QF-PCR and aCGH as part of the routine clinical evaluation. RESULTS: Chromosome aberrations were detected in 52/73 POCs (71.2%), of which 41 (56.2%) were identified by QF-PCR and an additional 11 (15.1%) by aCGH. Numerical aberrations constituted 92.3% of abnormalities, with trisomies as the most common subtype (72.9%). Causative structural aberrations were found in three samples (5.8%). The frequency of chromosome aberrations was not dependent on the number of previous miscarriages, whereas it significantly increased with advanced maternal age. CONCLUSION: Our results confirm that chromosome aberrations are the most common cause of RM and that QF-PCR and aCGH combination should be included in the routine genetic analysis of POCs of couples with miscarriage.


Subject(s)
Abortion, Habitual/genetics , Chromosome Aberrations , Chromosome Disorders/diagnosis , Comparative Genomic Hybridization/methods , Real-Time Polymerase Chain Reaction/methods , Adult , Chromosome Aberrations/classification , Female , Fluorometry , Humans , Karyotyping , Maternal Age , Pregnancy , Retrospective Studies
9.
Genes (Basel) ; 10(5)2019 05 13.
Article in English | MEDLINE | ID: mdl-31086101

ABSTRACT

Micronuclei research has regained its popularity due to the realization that genome chaos, a rapid and massive genome re-organization under stress, represents a major common mechanism for punctuated cancer evolution. The molecular link between micronuclei and chromothripsis (one subtype of genome chaos which has a selection advantage due to the limited local scales of chromosome re-organization), has recently become a hot topic, especially since the link between micronuclei and immune activation has been identified. Many diverse molecular mechanisms have been illustrated to explain the causative relationship between micronuclei and genome chaos. However, the newly revealed complexity also causes confusion regarding the common mechanisms of micronuclei and their impact on genomic systems. To make sense of these diverse and even conflicting observations, the genome theory is applied in order to explain a stress mediated common mechanism of the generation of micronuclei and their contribution to somatic evolution by altering the original set of information and system inheritance in which cellular selection functions. To achieve this goal, a history and a current new trend of micronuclei research is briefly reviewed, followed by a review of arising key issues essential in advancing the field, including the re-classification of micronuclei and how to unify diverse molecular characterizations. The mechanistic understanding of micronuclei and their biological function is re-examined based on the genome theory. Specifically, such analyses propose that micronuclei represent an effective way in changing the system inheritance by altering the coding of chromosomes, which belongs to the common evolutionary mechanism of cellular adaptation and its trade-off. Further studies of the role of micronuclei in disease need to be focused on the behavior of the adaptive system rather than specific molecular mechanisms that generate micronuclei. This new model can clarify issues important to stress induced micronuclei and genome instability, the formation and maintenance of genomic information, and cellular evolution essential in many common and complex diseases such as cancer.


Subject(s)
Genomic Instability/genetics , Micronucleus, Germline/genetics , Micronucleus, Germline/physiology , Chromosome Aberrations/classification , Chromothripsis , Databases, Genetic , Evolution, Molecular , Genome/genetics , Genomic Instability/physiology , Genomics/methods , Heredity/genetics , Humans , Neoplasms/genetics , Wills
10.
J Assist Reprod Genet ; 36(7): 1471-1479, 2019 Jul.
Article in English | MEDLINE | ID: mdl-31104291

ABSTRACT

PURPOSE: Infertility is estimated to affect 15% of couples, having chromosome abnormalities an important role in its etiology. The main objective of this work was to access the reproductive success of ART in infertile couples with chromosomal abnormalities comparing to a control group with normal karyotype. METHODS: A 7-year retrospective karyotype analysis of infertile couples was done. Data regarding type of infertility, couples' ages, ART performed, and their reproductive success were obtained. Adjusted odds ratio (OR) were used to estimate magnitude of association between the reproductive success and the different groups. RESULTS: We found a prevalence of 7.83% of chromosome abnormalities in our population (233 couples out of 2989). Chromosomal anomalies were found in 82 men (34.75%) and 154 women (65.25%), with low-grade mosaicism being the most prevalent (50.85%), followed by autosomal translocations (17.37%) and sex chromosomes abnormalities (13.56%). Only 2359 couples were treated with ART. There was a non-significant lower reproductive success rate in the cases (OR = 0.899, p = 0.530) with IVF providing the higher success rate. In general, female carriers of chromosome anomalies had a higher success rate, although not significant. CONCLUSION: Although the differences regarding success rate between groups were not found statistically significant, we still advocate that cytogenetic analysis should be performed routinely in all infertile couples namely before ART. This might help deciding the best treatment options including Preimplantation Genetic Testing for aneuploidies or structural rearrangements and minimize the risk of transmission of anomalies to the offspring.


Subject(s)
Chromosome Aberrations , Chromosome Disorders/epidemiology , Infertility, Male/genetics , Reproductive Techniques, Assisted , Adult , Aneuploidy , Chromosome Aberrations/classification , Chromosome Disorders/pathology , Chromosome Disorders/rehabilitation , Female , Fertilization in Vitro , Genetic Testing , Humans , Infertility, Male/epidemiology , Infertility, Male/pathology , Karyotyping , Male , Pregnancy , Pregnancy Outcome , Sperm Injections, Intracytoplasmic
11.
Nat Rev Clin Oncol ; 15(7): 409-421, 2018 07.
Article in English | MEDLINE | ID: mdl-29686421

ABSTRACT

Multiple myeloma (MM) is a plasma cell neoplasm that accounts for 2% of all haematological malignancies and predominantly affects older individuals (with a median age at diagnosis of 65-70 years). MM is consistently preceded by the clinically recognized precancerous stages monoclonal gammopathy of undetermined significance and smouldering MM. Thus far, MM has been considered as a single disease entity, but the clinical presentation, response to treatment, and survival outcomes of patients with MM are quite heterogeneous and highly dependent on a set of chromosomal abnormalities that can be identified in nearly all of them. These alterations include primary cytogenetic abnormalities, such as translocations involving chromosome 14q and trisomies of odd-numbered chromosomes, as well as secondary abnormalities, such as deletion of chromosome 17p and amplification of chromosome 1q. The aetiology of myeloma is poorly understood, although different nonoverlapping disease entities can be defined on the basis of their specific primary cytogenetic abnormalities, which have a major role in determining clinical behaviour. This classification might enable the development of better treatment strategies focused on the underlying biology of each specific subtype. Herein, we describe treatment approaches that incorporate the current standard of care for patients with MM along with recommended alterations or improvements that might provide additional clinical benefit for certain subgroups of patients.


Subject(s)
Monoclonal Gammopathy of Undetermined Significance/genetics , Multiple Myeloma/genetics , Multiple Myeloma/therapy , Translocation, Genetic , Age Factors , Aged , Chromosome Aberrations/classification , Chromosome Aberrations/drug effects , Chromosome Deletion , Chromosomes, Human, Pair 14/genetics , Humans , Monoclonal Gammopathy of Undetermined Significance/pathology , Monoclonal Gammopathy of Undetermined Significance/therapy , Multiple Myeloma/classification , Multiple Myeloma/pathology
12.
BJOG ; 125(4): 414-420, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29220118

ABSTRACT

Chromosome abnormalities account for half of the recorded miscarriages. Data from cytogenetic analysis of the products of conception (POC) in miscarriages are reviewed in the paper. Genetic analysis of POC allows patients to be given prognostic information. Molecular genetic techniques can overcome the pitfalls of conventional karyotyping, such as culture failure and trace submicroscopic abnormalities. We compare the pros and cons when these technologies are applied to the analysis of POC after miscarriage. Guidance is also provided for future clinical applications. The objective of the review is to help clinicians understand the limitations and to optimise the usefulness of genetic analysis of POC. TWEETABLE ABSTRACT: Genetics and POC of miscarriage.


Subject(s)
Aborted Fetus , Abortion, Habitual , Chromosome Aberrations/classification , Cytogenetic Analysis/methods , Abortion, Habitual/diagnosis , Abortion, Habitual/genetics , Female , Genetic Testing/methods , Humans , Pregnancy , Prognosis
13.
Cytometry A ; 91(6): 622-632, 2017 06.
Article in English | MEDLINE | ID: mdl-27144669

ABSTRACT

Multiplex-fluorescence in situ hybridization (M-FISH) is a chromosome imaging technique which can be used to detect chromosomal abnormalities such as translocations, deletions, duplications, and inversions. Chromosome classification from M-FISH imaging data is a key step to implement the technique. In the classified M-FISH image, each pixel in a chromosome is labeled with a class index and drawn with a pseudo-color so that geneticists can easily conduct diagnosis, for example, identifying chromosomal translocations by examining color changes between chromosomes. However, the information of pixels in a neighborhood is often overlooked by existing approaches. In this work, we assume that the pixels in a patch belong to the same class and use the patch to represent the center pixel's class information, by which we can use the correlations of neighboring pixels and the structural information across different spectral channels for the classification. On the basis of assumption, we propose a patch-based classification algorithm by using higher order singular value decomposition (HOSVD). The developed method has been tested on a comprehensive M-FISH database that we established, demonstrating improved performance. When compared with other pixel-wise M-FISH image classifiers such as fuzzy c-means clustering (FCM), adaptive fuzzy c-means clustering (AFCM), improved adaptive fuzzy c-means clustering (IAFCM), and sparse representation classification (SparseRC) methods, the proposed method gave the highest correct classification ratio (CCR), which can translate into improved diagnosis of genetic diseases and cancers. © 2016 International Society for Advancement of Cytometry.


Subject(s)
Algorithms , Chromosomes, Human/ultrastructure , Image Interpretation, Computer-Assisted/methods , In Situ Hybridization, Fluorescence/methods , Karyotyping/methods , Chromosome Aberrations/classification , Color , Databases, Factual , Humans , Staining and Labeling/methods
15.
Einstein (Sao Paulo) ; 14(1): 30-4, 2016.
Article in English, Portuguese | MEDLINE | ID: mdl-27074231

ABSTRACT

OBJECTIVE: To investigate chromosomal abnormalities by CGH-array in patients with dysmorphic features and intellectual disability with normal conventional karyotype. METHODS: Retrospective study, carried out from January 2012 to February 2014, analyzing the CGH-array results of 39 patients. RESULTS: Twenty-six (66.7%) patients had normal results and 13 (33.3%) showed abnormal results - in that, 6 (15.4%) had pathogenic variants, 6 (15.4%) variants designated as uncertain and 1 (2.5%) non-pathogenic variants. CONCLUSION: The characterization of the genetic profile by CGH-array in patients with intellectual disability and dysmorphic features enabled making etiologic diagnosis, followed by genetic counseling for families and specific treatment.


Subject(s)
Chromosome Aberrations/classification , Chromosomes, Human, Pair 6/genetics , Comparative Genomic Hybridization/methods , Intellectual Disability/genetics , Adolescent , Child , Child, Preschool , Female , Humans , Karyotype , Male , Retrospective Studies , Young Adult
16.
Blood ; 127(24): 2955-62, 2016 06 16.
Article in English | MEDLINE | ID: mdl-27002115

ABSTRACT

The International Myeloma Working Group consensus updates the definition for high-risk (HR) multiple myeloma based on cytogenetics Several cytogenetic abnormalities such as t(4;14), del(17/17p), t(14;16), t(14;20), nonhyperdiploidy, and gain(1q) were identified that confer poor prognosis. The prognosis of patients showing these abnormalities may vary with the choice of therapy. Treatment strategies have shown promise for HR cytogenetic diseases, such as proteasome inhibition in combination with lenalidomide/pomalidomide, double autologous stem cell transplant plus bortezomib, or combination of immunotherapy with lenalidomide or pomalidomide. Careful analysis of cytogenetic subgroups in trials comparing different treatments remains an important goal. Cross-trial comparisons may provide insight into the effect of new drugs in patients with cytogenetic abnormalities. However, to achieve this, consensus on definitions of analytical techniques, proportion of abnormal cells, and treatment regimens is needed. Based on data available today, bortezomib and carfilzomib treatment appear to improve complete response, progression-free survival, and overall survival in t(4;14) and del(17/17p), whereas lenalidomide may be associated with improved progression-free survival in t(4;14) and del(17/17p). Patients with multiple adverse cytogenetic abnormalities do not benefit from these agents. FISH data are implemented in the revised International Staging System for risk stratification.


Subject(s)
Multiple Myeloma/therapy , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Bortezomib , Chromosome Aberrations/classification , Combined Modality Therapy , Consensus , Cytogenetics , Hematopoietic Stem Cell Transplantation , Humans , Lenalidomide , Multiple Myeloma/classification , Multiple Myeloma/genetics , Multiple Myeloma/mortality , Prognosis , Risk Factors , Thalidomide/analogs & derivatives , Transplantation, Autologous
17.
Einstein (Säo Paulo) ; 14(1): 30-34, Jan.-Mar. 2016. tab, graf
Article in English | LILACS | ID: lil-778498

ABSTRACT

ABSTRACT Objective To investigate chromosomal abnormalities by CGH-array in patients with dysmorphic features and intellectual disability with normal conventional karyotype. Methods Retrospective study, carried out from January 2012 to February 2014, analyzing the CGH-array results of 39 patients. Results Twenty-six (66.7%) patients had normal results and 13 (33.3%) showed abnormal results - in that, 6 (15.4%) had pathogenic variants, 6 (15.4%) variants designated as uncertain and 1 (2.5%) non-pathogenic variants. Conclusion The characterization of the genetic profile by CGH-array in patients with intellectual disability and dysmorphic features enabled making etiologic diagnosis, followed by genetic counseling for families and specific treatment.


RESUMO Objetivo Avaliar microalterações cromossômicas por CGH-array em portadores de dismorfias e deficiência intelectual com cariótipo normal. Métodos Estudo retrospectivo, realizado no período de janeiro de 2012 a fevereiro de 2014, analisando os resultados de CGH-array de 39 pacientes. Resultados Apresentaram resultados normais 26 (66,7%) pacientes; 13 (33,3%) tiveram resultados alterados, a saber: 6 (15,4%) com variantes patogênicas, 6 (15,4%) com variantes pertencentes à categoria designada como incerta, e 1 (2,5%) com variantes não patogênicas. Conclusão A caracterização do perfil genético por CGH-array nos pacientes com deficiência intelectual e dismorfias possibilitou complementar o diagnóstico etiológico, permitindo a realização do aconselhamento genético para as famílias e tratamento específico.


Subject(s)
Humans , Male , Female , Child, Preschool , Child , Adolescent , Young Adult , Chromosomes, Human, Pair 6/genetics , Chromosome Aberrations/classification , Comparative Genomic Hybridization/methods , Intellectual Disability/genetics , Retrospective Studies , Karyotype
18.
Gene ; 589(2): 112-7, 2016 Sep 10.
Article in English | MEDLINE | ID: mdl-26850130

ABSTRACT

It is 60years since the discovery of the correct number of chromosomes in 1956; the field of cytogenetics had evolved. The late evolution of this field with respect to other fields is primarily due to the underdevelopment of lenses and imaging techniques. With the advent of the new technologies, especially automation and evolution of advanced compound microscopes, cytogenetics drastically leaped further to greater heights. This review describes the historic events that had led to the development of human cytogenetics with a special attention about the history of cytogenetics in India, its present status, and future. Apparently, this review provides a brief account into the insights of the early laboratory establishments, funding, and the German collaborations. The details of the Indian cytogeneticists establishing their labs, promoting the field, and offering the chromosomal diagnostic services are described. The detailed study of chromosomes helps in increasing the knowledge of the chromosome structure and function. The delineation of the chromosomal rearrangements using cytogenetics and molecular cytogenetic techniques pays way in identifying the molecular mechanisms involved in the chromosomal rearrangement. Although molecular cytogenetics is greatly developing, the conventional cytogenetics still remains the gold standard in the diagnosis of various numerical chromosomal aberrations and a few structural aberrations. The history of cytogenetics and its importance even in the era of molecular cytogenetics are discussed.


Subject(s)
Chromosome Aberrations/classification , Chromosomes, Human/ultrastructure , Cytogenetics/history , Diagnostic Services/history , Chromosomes, Human/chemistry , Comparative Genomic Hybridization/history , Comparative Genomic Hybridization/methods , Cytogenetics/methods , Diagnostic Services/organization & administration , High-Throughput Nucleotide Sequencing/history , High-Throughput Nucleotide Sequencing/methods , History, 19th Century , History, 20th Century , History, 21st Century , Humans , In Situ Hybridization, Fluorescence/history , In Situ Hybridization, Fluorescence/methods , India , Karyotyping/history , Karyotyping/methods
19.
Vopr Onkol ; 62(4): 429-38, 2016.
Article in Russian | MEDLINE | ID: mdl-30475526

ABSTRACT

Over the past decades the studies have greatly improved our understanding of the molecular basis of multiple myeloma (MM) and mechanisms of disease progression. The majority of the most widespread chromosomal aberrations, revealing in MM, has independent predictive value and influence on a choice of optimal treatment. There were observed 190 MM patients in hematologic hospitals of St. Petersburg. Genetic anomalies (GA) were detected at 3l,3% of patients and did not depend on their age. Patients with ISS III had a detectability of GA higher than with ISS II and ISS I (48,°% (24/5°), 2l,2% (7/33) and 27,6% (8/29)). Translocation t(ll;l4) was found in 23,3% (3O/129) patients; dell3q - 20,8% (27/13°); dell7p - at 8,4% (7/83); t(4;l4) - at 6,9% (9/13O), that allowed to stratify patients in groups of risk according to mSMART version l. O and 2. O. Median overall survival (OS) modified mSMART l. O in group of standard risk was 7° months, high risk - 47,l months. Median OS mSMART 2. O in group of standard risk was 7° months, intermediate risk - 47 months, high risk - 45 months. OS did not depend on age, clinical manifestations, treatment and other factors.


Subject(s)
Chromosome Aberrations/classification , Multiple Myeloma/diagnosis , Multiple Myeloma/genetics , Translocation, Genetic/genetics , Adult , Aged , Aged, 80 and over , Chromosomes/genetics , Female , Humans , Karyotype , Male , Middle Aged , Multiple Myeloma/classification , Multiple Myeloma/pathology
20.
Tsitol Genet ; 49(3): 33-9, 2015.
Article in Russian | MEDLINE | ID: mdl-26214903

ABSTRACT

To assess the frequency and structure of chromosomal abnormalities in patients with infertility, a retrospective analysis of cytogenetic studies of 3414 patients (1741 females and 1673 males), referred to the Clinic of reproductive medicine "Nadiya" from 2007 to 2012, was performed. Chromosomal abnormalities were detected in 2.37% patients: 2.79% in males and 1.95% in females. Balanced structural chromosomal abnormalities prevailed over numerical abnormalities and corresponded to 80.2% of all chromosomal abnormalities detected in the studied group. Sex chromosome abnormalities made up 23.5% of chromosomal pathology (19/81) and included gonosomal aneuploidies in 84% of cases (16/19) and structural abnormalities of chromosome Y in 16% of cases (3/19). The low level sex chromosome mosaicism was detected with the frequency of 0.55%. Our results highlight the importance of cytogenetic studies in patients seeking infertility treatment by assisted reproductive technologies, since an abnormal finding not only provide a firm diagnosis to couples with infertility, but also influences significantly the approach to infertility treatment in such patients.


Subject(s)
Chromosome Aberrations/statistics & numerical data , Infertility, Female/genetics , Infertility, Male/genetics , Sex Chromosomes/chemistry , Adult , Chromosome Aberrations/classification , Female , Humans , Infertility, Female/diagnosis , Infertility, Female/pathology , Infertility, Male/diagnosis , Infertility, Male/pathology , Karyotyping , Male , Reproductive Medicine , Retrospective Studies , Sex Chromosomes/pathology
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