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1.
PLoS One ; 7(7): e39101, 2012.
Article in English | MEDLINE | ID: mdl-22792164

ABSTRACT

BACKGROUND: Women with low grade squamous intraepithelial lesions (LSIL) at cervical cancer screening are currently referred for further diagnostic work up despite 80% having no precancerous lesion. The primary purpose of this study is to measure the test characteristics of 3q26 chromosome gain (3q26 gain) as a host marker of carcinogenesis in women with LSIL. A negative triage test may allow these women to be followed by cytology alone without immediate referral to colposcopy. METHODS AND FINDINGS: A historical prospective study was designed to measure 3q26 gain from the archived liquid cytology specimens diagnosed as LSIL among women attending colposcopy between 2007 and 2009. 3q26 gain was assessed on the index liquid sample; and sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were measured at immediate triage and at 6-16 months after colposcopic biopsy. The sensitivity of 3q26 gain measured at immediate triage from automated and manually reviewed tests in 65 non-pregnant unique women was 70% (95% CI: 35, 93) with a NPV of 89% (95% CI: 78, 96). The sensitivity and NPV increased to 80% (95% CI: 28, 99) and 98% (95% CI: 87, 100), respectively, when only the automated method of detecting 3q26 gain was used. CONCLUSIONS: 3q26 gain demonstrates high sensitivity and NPV as a negative triage test for women with LSIL, allowing possible guideline changes to routine surveillance instead of immediate colposcopy. Prospective studies are ongoing to establish the sensitivity, specificity, PPV and NPV of 3q26 gain for LSIL over time.


Subject(s)
Chromosomes, Human, Pair 3 , Gene Amplification , Triage , Uterine Cervical Dysplasia/diagnosis , Uterine Cervical Dysplasia/genetics , Adult , Colposcopy , Female , Humans , Prospective Studies , Sensitivity and Specificity , Young Adult
2.
Am J Hum Genet ; 87(2): 209-18, 2010 Aug 13.
Article in English | MEDLINE | ID: mdl-20673865

ABSTRACT

Palindrome-mediated genomic instability has been associated with chromosomal translocations, including the recurrent t(11;22)(q23;q11). We report a syndrome characterized by extremity anomalies, mild dysmorphia, and intellectual impairment caused by 3:1 meiotic segregation of a previously unrecognized recurrent palindrome-mediated rearrangement, the t(8;22)(q24.13;q11.21). There are at least ten prior reports of this translocation, and nearly identical PATRR8 and PATRR22 breakpoints were validated in several of these published cases. PCR analysis of sperm DNA from healthy males indicates that the t(8;22) arises de novo during gametogenesis in some, but not all, individuals. Furthermore, demonstration that de novo PATRR8-to-PATRR11 translocations occur in sperm suggests that palindrome-mediated translocation is a universal mechanism producing chromosomal rearrangements.


Subject(s)
Chromosomes, Human, Pair 22/genetics , Chromosomes, Human, Pair 8/genetics , Inverted Repeat Sequences/genetics , Meiosis/genetics , Nondisjunction, Genetic , Translocation, Genetic/genetics , AT Rich Sequence/genetics , Adolescent , Adult , Base Sequence , Child , Child, Preschool , Chromosome Breakage , Female , Gene Dosage/genetics , Genotype , Health , Humans , Male , Molecular Sequence Data , Phenotype , Sequence Analysis, DNA , Spermatogenesis/genetics , Spermatozoa/metabolism
3.
Am J Obstet Gynecol ; 202(6): 581.e1-5, 2010 Jun.
Article in English | MEDLINE | ID: mdl-20171606

ABSTRACT

OBJECTIVE: The chromosome 3q26 region is a biomarker for cervical cancer. Women with low-grade squamous intraepithelial lesions (LSIL) currently are referred for immediate colposcopy. The objective of this study was to determine the negative predictive value of the 3q26 amplification test for the persistence or regression of LSIL. STUDY DESIGN: Archival thin layer cytologic slides of 47 women (14-67 years old) with LSIL were linked to histologic and cytologic end points. To determine 3q status, the slides were hybridized for the chromosome 3q26 region and for the centromere of chromosome 7, as a control, with the use of the standard fluorescent in situ hybridization methods. RESULTS: The negative predictive value of 3q26 gain for the development of cervical intraepithelial neoplasia grade 2/3 within 1 year was 93% (95% confidence interval, 68- 100); after 21 months, its negative predictive value was 100% (95% confidence interval, 29-100). CONCLUSION: The 3q26 gain might help identify women with LSIL who do not need colposcopy.


Subject(s)
Chromosomes, Human, Pair 3/genetics , Papillomavirus Infections/genetics , Uterine Cervical Dysplasia/genetics , Uterine Cervical Neoplasms/genetics , Colposcopy , Early Detection of Cancer , Female , Humans , In Situ Hybridization, Fluorescence , Papillomavirus Infections/pathology , Predictive Value of Tests , Retrospective Studies , Uterine Cervical Dysplasia/pathology , Uterine Cervical Neoplasms/pathology , Vaginal Smears
4.
Gynecol Oncol ; 114(1): 80-3, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19394683

ABSTRACT

OBJECTIVE: Physicians have few resources for determining which LSIL will progress to HSIL or regress. Recently the chromosome 3q26 region was found to be amplified in patients with cervical cancer. The frequency of this 3q gain increased with severity of dysplasia. The primary objective of this study was to evaluate an automated FISH assay for detection of 3q gain in liquid cytology samples as a potential tool for risk stratification and triaging. METHODS: Slides prepared from 257 liquid cytology specimens (97 Negative, 135 LSIL 25 HSIL) were hybridized with a single-copy probe for the chromosome 3q26 region and a probe for the centromeric alpha-repeat sequence of chromosome 7, using standard FISH methods. Using automated analysis, the total number of nuclei and the number of nuclei with >2 signals for 3q26 were determined, using a 20x objective. The nuclei were rank ordered based on number of 3q26 FISH signals. The 800 nuclei with the highest number of signals were scored using both FISH probes and nuclei with increased numbers of 3q signals were enumerated. RESULTS AND CONCLUSIONS: Analysis of 257 specimens demonstrated that a fully automated FISH scoring system can detect 3q gain in liquid cytology samples. A fully automated method for determination of 3q gain in liquid cytology may be the assay necessary to implement routine testing. Additional studies to validate the utility of this technology are needed.


Subject(s)
Cervix Uteri/pathology , Chromosomes, Human, Pair 3 , Gene Dosage , Uterine Cervical Dysplasia/genetics , Uterine Cervical Neoplasms/genetics , Cervix Uteri/physiopathology , Chromosome Mapping , Female , Genetic Markers , Humans , In Situ Hybridization, Fluorescence , Uterine Cervical Dysplasia/diagnosis , Uterine Cervical Dysplasia/pathology , Uterine Cervical Neoplasms/diagnosis , Uterine Cervical Neoplasms/pathology , Vaginal Smears
5.
Genome Res ; 17(4): 470-81, 2007 Apr.
Article in English | MEDLINE | ID: mdl-17351131

ABSTRACT

Constitutional translocations at the same 22q11.21 low copy repeat B (LCR-B) breakpoint involved in the recurrent t(11;22) are relatively abundant. A novel 46,XY,t(8;22)(q24.13;q11.21) rearrangement was investigated to determine whether the recurrent LCR-B breakpoint is involved. Investigations demonstrated an inversion of the 3Mb region typically deleted in patients with the 22q11.2 deletion syndrome. The 22q11.21 inversion appears to be mediated by low copy repeats, and is presumed to have taken place prior to translocation with 8q24.13. Despite predictions based on inversions observed in other chromosomes harboring low copy repeats, this 22q11.2 inversion has not been observed previously. The current studies utilize novel laser microdissection and MLPA (multiplex ligation-dependent probe amplification) approaches, as adjuncts to FISH, to map the breakpoints of the complex rearrangements of 22q11.21 and 8q24.21. The t(8;22) occurs between the recurrent site on 22q11.21 and an AT-rich site at 8q24.13, making it the fifth different chromosomal locus characterized at the nucleotide level engaged in a translocation with the unstable recurrent breakpoint at 22q11.21. Like the others, this breakpoint occurs at the center of a palindromic sequence. This sequence appears capable of forming a perfect 145 bp stem-loop. Remarkably, this site appears to have been involved in a previously reported t(3;8) occurring between 8q24.13 and FRA3B on 3p14.2. Further, the fragile site-like nature of all of the breakpoint sites involved in translocations with the recurrent site on 22q11.21, suggests a mechanism based on delay of DNA replication in the initiation of these chromosomal rearrangements.


Subject(s)
Chromosomes, Human, Pair 11/genetics , Chromosomes, Human, Pair 22/genetics , Repetitive Sequences, Nucleic Acid , Translocation, Genetic , AT Rich Sequence , Base Sequence , Chromosome Breakage , Chromosome Deletion , DNA/chemistry , DNA/genetics , DNA Probes/genetics , Family Health , Female , Humans , In Situ Hybridization, Fluorescence/methods , Male , Models, Genetic , Molecular Sequence Data , Nucleic Acid Conformation , Polymerase Chain Reaction/methods , Sequence Analysis, DNA , Syndrome
6.
Br J Haematol ; 129(4): 520-30, 2005 May.
Article in English | MEDLINE | ID: mdl-15877734

ABSTRACT

Summary Interphase fluorescence in situ hybridization (iFISH) was used independently to reveal chromosomal abnormalities of prognostic importance in a large, consecutive series of children (n = 2367) with acute lymphoblastic leukaemia (ALL). The fusions, TEL/AML1 and BCR/ABL, and rearrangements of the MLL gene occurred at frequencies of 22% (n = 447/2027) (25% in B-lineage ALL), 2% (n = 43/2027) and 2% (n = 47/2016) respectively. There was considerable variation in iFISH signal patterns both between and within patient samples. The TEL/AML1 probe showed the highest incidence of variation (59%, n = 524/884), which included 38 (2%) patients with clustered, multiple copies of AML1. We were thus able to define amplification of AML1 as a new recurrent abnormality in ALL, associated with a poor prognosis. Amplification involving the ABL gene, a rare recurrent abnormality confined to T ALL patients, was identified for the first time. The use of centromeric probes revealed significant hidden high hyperdiploidy of 33% and 59%, respectively, in patients with normal (n = 21/64) or failed (n = 32/54) cytogenetic results. The iFISH contributed significantly to the high success rate of 91% (n = 2114/2323) and the remarkable abnormality detection rate of 89% (n = 1879/2114). This study highlights the importance of iFISH as a complementary tool to cytogenetics in routine screening for significant chromosomal abnormalities in ALL.


Subject(s)
Chromosome Aberrations , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Adolescent , Child , Child, Preschool , Core Binding Factor Alpha 2 Subunit , Cytogenetic Analysis , DNA-Binding Proteins/genetics , Fusion Proteins, bcr-abl/genetics , Gene Amplification , Gene Rearrangement , Genes, abl , Histone-Lysine N-Methyltransferase , Humans , In Situ Hybridization, Fluorescence , Infant , Interphase , Myeloid-Lymphoid Leukemia Protein , Oncogene Proteins, Fusion/genetics , Prognosis , Proto-Oncogenes/genetics , Reverse Transcriptase Polymerase Chain Reaction , Transcription Factors/genetics
7.
Genes Chromosomes Cancer ; 43(1): 54-71, 2005 May.
Article in English | MEDLINE | ID: mdl-15704129

ABSTRACT

This study was undertaken in order to compare the interphase and metaphase cytogenetics of 28 patients with ETV6/RUNX1 positive acute lymphoblastic leukemia, at diagnosis and relapse. The median time to relapse was 26 months. The significant fusion positive population heterogeneity revealed at interphase by a commercial probe for ETV6/RUNX1 fusion has not been described before. Six diagnostic samples had a single abnormal population; others had up to five each, which differed in the numbers of RUNX1 signals, and in the retention or loss of the second ETV6 signal. In contrast, the number of fusion signals was more constant. At relapse, there were fewer populations; the largest or unique clone was sometimes a re-emergence of a minor, diagnostic one, with a retained copy of ETV6 and the most RUNX1 signals. Abnormal, fusion negative clones were identified in bone marrow samples at extra-medullary relapse. Variant three or four-way translocations, which involved chromosomes 12 and 21, were prominent among the complex rearrangements revealed by metaphase FISH. The frequency of their occurrence at diagnosis and reappearance at relapse, sometimes accompanied by minor clonal evolution, was another new observation. Other recurrent cytogenetic features included a second copy of the fusion signal in six cases, partial duplication of the long arm of the X chromosome in two cases, and trisomy 10 in three cases. In comparing our data with previously reported cases, a picture is beginning to emerge of certain diagnostic features, which may provide circumstantial evidence of an increased risk of relapse.


Subject(s)
Artificial Gene Fusion , DNA-Binding Proteins/genetics , Nuclear Proteins/genetics , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Proto-Oncogene Proteins/genetics , Repressor Proteins/genetics , Transcription Factors/genetics , Adolescent , Adult , Child , Child, Preschool , Chromosome Mapping , Core Binding Factor Alpha 2 Subunit , Female , Humans , In Situ Hybridization, Fluorescence , Infant , Karyotyping , Male , Middle Aged , Precursor Cell Lymphoblastic Leukemia-Lymphoma/diagnosis , Prognosis , Proto-Oncogene Proteins c-ets , Recurrence , ETS Translocation Variant 6 Protein
8.
Genes Chromosomes Cancer ; 39(1): 88-92, 2004 Jan.
Article in English | MEDLINE | ID: mdl-14603446

ABSTRACT

The recurrent t(14;19)(q32;q13) translocation associated with chronic B-cell lymphoproliferative disorders, such as atypical chronic lymphocytic leukemia, results in the juxtaposition of the IGH@ and BCL3 genes and subsequent overexpression of BCL3. We report six patients with B-cell precursor acute lymphoblastic leukemia who have a cytogenetically identical translocation with different breakpoints at the molecular level. Fluorescence in situ hybridization with locus-specific probes confirmed the involvement of the IGH@ gene but showed that the breakpoint on 19q13 lay outside the region documented in t(14;19)(q32;q13)-positive chronic lymphocytic leukemia. This newly described translocation constitutes a distinct cytogenetic subgroup that is confined to older children and younger adults with B-cell precursor acute lymphoblastic leukemia.


Subject(s)
Chromosomes, Human, Pair 14/genetics , Chromosomes, Human, Pair 19/genetics , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics , Adolescent , Adult , Child , Female , Humans , Male , Translocation, Genetic/genetics
9.
Genes Chromosomes Cancer ; 37(4): 406-11, 2003 Aug.
Article in English | MEDLINE | ID: mdl-12800152

ABSTRACT

Previous studies on concordant acute lymphoblastic leukemia (ALL) in identical twins have identified the leukemia as monoclonal with MLL or ETV6-RUNX1 gene fusion as early or initiating events in utero. In the latter case, postnatal latency is associated with secondary genetic events such as ETV6 deletion. We describe here a pair of infant twins with concordant acute monoblastic leukemia (AML). They are a unique pair in that their leukemia blasts display extensive intraclonal chromosomal diversity. Comparison of the leukemic cells between the two twins by karyotype and fluorescence in situ hybridization identifies a common or shared stem line and extensive subclonal diversity for which the twins' leukemic populations are divergent. This case of leukemia illustrates in utero initiation with early imposition of chromosomal instability, the progressively divergent evolution of which can be mapped in the twins into pre- and postnatal periods.


Subject(s)
Diseases in Twins/embryology , Diseases in Twins/genetics , Leukemia, Monocytic, Acute/embryology , Leukemia, Monocytic, Acute/genetics , Twins, Monozygotic/genetics , Chromosome Aberrations , Chromosome Deletion , Clone Cells , DNA-Binding Proteins/genetics , Humans , Infant , Male , Proto-Oncogene Proteins c-ets , Repressor Proteins/genetics , ETS Translocation Variant 6 Protein
10.
Blood ; 102(8): 2756-62, 2003 Oct 15.
Article in English | MEDLINE | ID: mdl-12829593

ABSTRACT

High hyperdiploidy (HeH) (51 to 65 chromosomes) is found in one third of children with acute lymphoblastic leukemia and is associated with a good prognosis. Cytogenetic features may further refine this prognosis and identify patients with a poor outcome. We examined the effect of sex, age, individual trisomies, modal number, and structural abnormalities on survival among 700 children with HeH. Univariate analysis showed that age. sex, +4, +10, +18, and a high modal number were associated with survival. Multivariate analysis however, revealed that only age, sex, +4, and +18 were independent indicators. Hazard scores for predicting relapse and mortality were constructed. Three risk groups with 5-year event-free survival (EFS) rates of 86%, 75%, and 50% (P <.0001) were identified. The high-risk group comprised boys older than 9 years, boys aged 1 through 9 years without +18, and girls older than 9 years without +18, while girls aged 1 through 9 years with +18 had the best EFS. In terms of mortality, those younger than age 10 years with both +4 and +18 had an improved survival (96% vs 84% at 5 years, P <.0001). These findings confirm that the outcome of children with HeH is heterogeneous and that specific trisomies can identify patients with the greatest and least risk of treatment failure.


Subject(s)
Diploidy , Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Adolescent , Age Factors , Child , Child, Preschool , Disease-Free Survival , Female , Humans , In Situ Hybridization, Fluorescence , Infant , Karyotyping , Male , Multivariate Analysis , Precursor Cell Lymphoblastic Leukemia-Lymphoma/mortality , Prognosis , Proportional Hazards Models , Sex Factors , Time Factors , Treatment Outcome , Trisomy
11.
Br J Haematol ; 120(6): 944-52, 2003 Mar.
Article in English | MEDLINE | ID: mdl-12648063

ABSTRACT

The cytogenetic picture in multiple myeloma (MM) is highly complex, from which non-random numerical and structural chromosomal changes have been identified. Specifically, translocations involving the immunoglobulin heavy chain gene (IGH) at 14q32 and either monosomy or deletions of chromosome 13 have been reported in a significant number of patients from both cytogenetic and interphase fluorescence in situ hybridization (FISH) studies. Importantly, these abnormalities of chromosome 13 have recently been associated with a poor prognosis. In view of the highly complex nature of the karyotypes in MM patients, interphase FISH results may be difficult to interpret. In this study, cytogenetics and/or interphase FISH were carried out on bone marrow samples or purified plasma cells from 37 MM patients. Abnormal karyotypes, characterized by multiplex FISH (M-FISH) were found in 11 patients, all of which were highly complex. Interphase FISH revealed translocations involving the IGH locus in 16 (43%) patients. The IGH/cyclin D1 (CCND1) gene fusion characteristic of the translocation, t(11;14)(q13;q32), was seen in 12 (32%) of these patients and other rearrangements of IGH in four (11%) patients. Fourteen patients had additional copies of chromosome 11. Twenty patients (54%) had 13q14 deletions, 10 of whom also had t(11;14) or another IGH translocation. By comparing cytogenetic and FISH results, this study has revealed that significant chromosomal abnormalities might be hidden within highly complex karyotypes. Therefore, extreme caution is required in the interpretation of interphase FISH results in MM, particularly in relation to certain abnormalities, such as 13q14 deletions, which have an impact on prognosis.


Subject(s)
Chromosome Aberrations , Multiple Myeloma/genetics , Adult , Aged , Aged, 80 and over , Case-Control Studies , Chromosomes, Human, Pair 11 , Chromosomes, Human, Pair 13 , Chromosomes, Human, Pair 14 , Cytogenetic Analysis , Female , Gene Deletion , Gene Rearrangement , Humans , Immunoglobulin Heavy Chains/genetics , In Situ Hybridization, Fluorescence , Interphase , Karyotyping , Male , Metaphase , Middle Aged , Prognosis , Translocation, Genetic
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