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Article ; Online: Mutation analysis of RAD51L1 (RAD51B/REC2) in multiple-case, non-BRCA1/2 breast cancer families.

Johnson, Julie / Healey, Sue / Khanna, Kum Kum / Chenevix-Trench, Georgia

2011 Volume 129, Issue 1, Page(s) 255–263

Abstract: Although a significant proportion of familial aggregation of breast cancer remains unexplained, many of the currently known breast cancer susceptibility genes, including BRCA1, BRCA2 and TP53, play a role in maintaining genome integrity by engaging in ... ...

Abstract	Although a significant proportion of familial aggregation of breast cancer remains unexplained, many of the currently known breast cancer susceptibility genes, including BRCA1, BRCA2 and TP53, play a role in maintaining genome integrity by engaging in DNA repair. RAD51L1 is one of the five RAD51 paralogs involved in homologous recombination (HR) repair of DNA double-strand breaks (DSBs); it also interacts directly with p53. Deleterious mutations have been found in one RAD51 paralog, RAD51C (RAD51L2), in non-BRCA1/2 breast and ovarian cancer families, which suggests that all five paralogs are strong candidate breast cancer susceptibility genes. A genome-wide association study (GWAS) has already identified a single nucleotide polymorphism (SNP) deep within intron 10 of RAD51L1 as a risk locus for breast cancer. Based on its biological functions and association with RAD51C, there is reason to suggest that RAD51L1 (RAD51B/REC2) may also contain high risk mutations in the gene that give rise to multiple-case breast cancer families. In order to investigate this hypothesis, we have used high resolution melt (HRM) analysis to screen RAD51L1 for germline mutations in 188 non-BRCA1/2 multiple-case breast cancer families and 190 controls. We identified a total of seven variants: one synonymous, three intronic, and three previously identified SNPs, but no truncating or nonsense changes. Therefore, our results suggest that RAD51L1 is unlikely to represent a high-penetrance breast cancer susceptibility gene.
MeSH term(s)	Alleles ; Base Sequence ; Breast Neoplasms/genetics ; DNA-Binding Proteins/genetics ; Female ; Gene Frequency/genetics ; Genes, BRCA1 ; Genes, BRCA2 ; Genetic Predisposition to Disease ; Humans ; Mutation/genetics ; Polymorphism, Single Nucleotide/genetics
Chemical Substances	DNA-Binding Proteins ; RAD51B protein, human
Language	English
Publishing date	2011-08
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-011-1539-6
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Article ; Online: Targeted massively parallel sequencing of a panel of putative breast cancer susceptibility genes in a large cohort of multiple-case breast and ovarian cancer families.

Li, Jun / Meeks, Huong / Feng, Bing-Jian / Healey, Sue / Thorne, Heather / Makunin, Igor / Ellis, Jonathan / Campbell, Ian / Southey, Melissa / Mitchell, Gillian / Clouston, David / Kirk, Judy / Goldgar, David / Chenevix-Trench, Georgia

Journal of medical genetics

2016 Volume 53, Issue 1, Page(s) 34–42

Abstract: Introduction: Gene panel testing for breast cancer susceptibility has become relatively cheap and accessible. However, the breast cancer risks associated with mutations in many genes included in these panels are unknown.: Methods: We performed custom- ...

Abstract	Introduction: Gene panel testing for breast cancer susceptibility has become relatively cheap and accessible. However, the breast cancer risks associated with mutations in many genes included in these panels are unknown. Methods: We performed custom-designed targeted sequencing covering the coding exons of 17 known and putative breast cancer susceptibility genes in 660 non-BRCA1/2 women with familial breast cancer. Putative deleterious mutations were genotyped in relevant family members to assess co-segregation of each variant with disease. We used maximum likelihood models to estimate the breast cancer risks associated with mutations in each of the genes. Results: We found 31 putative deleterious mutations in 7 known breast cancer susceptibility genes (TP53, PALB2, ATM, CHEK2, CDH1, PTEN and STK11) in 45 cases, and 22 potential deleterious mutations in 31 cases in 8 other genes (BARD1, BRIP1, MRE11, NBN, RAD50, RAD51C, RAD51D and CDK4). The relevant variants were then genotyped in 558 family members. Assuming a constant relative risk of breast cancer across age groups, only variants in CDH1, CHEK2, PALB2 and TP53 showed evidence of a significantly increased risk of breast cancer, with some supportive evidence that mutations in ATM confer moderate risk. Conclusions: Panel testing for these breast cancer families provided additional relevant clinical information for <2% of families. We demonstrated that segregation analysis has some potential to help estimate the breast cancer risks associated with mutations in breast cancer susceptibility genes, but very large case-control sequencing studies and/or larger family-based studies will be needed to define the risks more accurately.
MeSH term(s)	Biomarkers, Tumor/genetics ; Computational Biology/methods ; Exons ; Female ; Genes, BRCA1 ; Genes, BRCA2 ; Genetic Association Studies ; Genetic Predisposition to Disease ; Genetic Testing ; Genotype ; Germ-Line Mutation ; Hereditary Breast and Ovarian Cancer Syndrome/diagnosis ; Hereditary Breast and Ovarian Cancer Syndrome/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mutation ; Odds Ratio ; Ovarian Neoplasms/diagnosis ; Ovarian Neoplasms/genetics ; Pedigree
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2016-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	220881-7
ISSN	1468-6244 ; 0022-2593
ISSN (online)	1468-6244
ISSN	0022-2593
DOI	10.1136/jmedgenet-2015-103452
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Article: A second case of intrauterine growth retardation and primary hypospadias associated with a trisomy 22 placenta but with biparental inheritance of chromosome 22 in the fetus.

Bryan, Jennifer / Peters, Michelle / Pritchard, Gary / Healey, Sue / Payton, Diane

Prenatal diagnosis

2001 Volume 22, Issue 2, Page(s) 137–140

Abstract: We report a case of severe intrauterine growth retardation (IUGR) and hypospadias in association with trisomy 22 diagnosed following chorionic villus sampling (CVS). Subsequent analysis of amniotic fluid cultures showed a normal male karyotype, 46,XY. As ...

Abstract	We report a case of severe intrauterine growth retardation (IUGR) and hypospadias in association with trisomy 22 diagnosed following chorionic villus sampling (CVS). Subsequent analysis of amniotic fluid cultures showed a normal male karyotype, 46,XY. As a previous case had been reported with similar abnormalities, in association with maternal uniparental disomy (UPD) 22, molecular studies were also performed. Microsatellite marker studies showed biparental inheritance. Follow-up studies after delivery showed a normal cell line in lymphocytes with the trisomy appearing to be confined to the placenta. The present case concurs with other earlier reports that maternal UPD for chromosome 22 has no impact on the phenotype. The features seen in the fetus are most likely the result of placental dysfunction due to trisomy, tissue-specific mosaicism and/or the effects of local growth restriction.
MeSH term(s)	Adult ; Amniocentesis ; Chorionic Villi Sampling ; Chromosomes, Human, Pair 22 ; Cytogenetic Analysis ; DNA/analysis ; Female ; Fetal Growth Retardation/diagnostic imaging ; Fetal Growth Retardation/genetics ; Genotype ; Gestational Age ; Humans ; Hypospadias/genetics ; Male ; Microsatellite Repeats ; Phenotype ; Placenta/pathology ; Pregnancy ; Trisomy ; Ultrasonography, Prenatal
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2001-09-04
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	82031-3
ISSN	1097-0223 ; 0197-3851
ISSN (online)	1097-0223
ISSN	0197-3851
DOI	10.1002/pd.260
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Article ; Online: Paclitaxel sensitivity in relation to ABCB1 expression, efflux and single nucleotide polymorphisms in ovarian cancer.

Gao, Bo / Russell, Amanda / Beesley, Jonathan / Chen, Xiao Qing / Healey, Sue / Henderson, Michelle / Wong, Mark / Emmanuel, Catherine / Galletta, Laura / Johnatty, Sharon E / Bowtell, David / Haber, Michelle / Norris, Murray / Harnett, Paul / Chenevix-Trench, Georgia / Balleine, Rosemary L / deFazio, Anna

Scientific reports

2014 Volume 4, Page(s) 4669

Abstract: ABCB1 (adenosine triphosphate-binding cassette transporter B1) mediates cellular elimination of many chemotherapeutic agents including paclitaxel, which is commonly used to treat ovarian cancer. A significant association between common single nucleotide ... ...

Abstract	ABCB1 (adenosine triphosphate-binding cassette transporter B1) mediates cellular elimination of many chemotherapeutic agents including paclitaxel, which is commonly used to treat ovarian cancer. A significant association between common single nucleotide polymorphisms (SNPs) in ABCB1 and progression-free survival has been reported in patients with ovarian cancer. Variable paclitaxel clearance due to genotype specific differences in ABCB1 activity in cancer cells and/or normal tissues may underlie the association. Using cell-based models, we evaluated the correlations between ABCB1 expression, polymorphisms, transporter activity and paclitaxel sensitivity in ovarian cancer (n = 10) and lymphoblastoid (n = 19) cell lines. Close associations between ABCB1 expression, transporter function and paclitaxel sensitivity were found in lymphoblastoid cell lines, although we could not demonstrate an association with common SNPs. In ovarian cancer cell lines, ABCB1 expression was low and the association between expression and function was lost. These results suggest that ABCB1 related survival difference in ovarian cancer patients is more likely to be due to differential whole body paclitaxel clearance mediated by normal cells rather than a direct effect on cancer cells.
MeSH term(s)	ATP Binding Cassette Transporter, Subfamily B/genetics ; Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; Female ; Genotype ; Humans ; Ovarian Neoplasms/drug therapy ; Ovarian Neoplasms/genetics ; Paclitaxel/pharmacology ; Polymorphism, Single Nucleotide/genetics
Chemical Substances	ABCB1 protein, human ; ATP Binding Cassette Transporter, Subfamily B ; Antineoplastic Agents ; Paclitaxel (P88XT4IS4D)
Language	English
Publishing date	2014-05-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep04669
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Article: Analysis of the transcription regulator, CNOT7, as a candidate chromosome 8 tumor suppressor gene in colorectal cancer.

Flanagan, James / Healey, Sue / Young, Joanne / Whitehall, Vicki / Chenevix-Trench, Georgia

International journal of cancer

2003 Volume 106, Issue 4, Page(s) 505–509

Abstract: Loss of heterozygosity (LOH) on the short arm of chromosome 8 occurs at high frequencies in many tumor types, including colorectal carcinoma. We have previously used microcell-mediated chromosome transfer (MMCT) to map an approximately 7.7 Mb colorectal ... ...

Abstract	Loss of heterozygosity (LOH) on the short arm of chromosome 8 occurs at high frequencies in many tumor types, including colorectal carcinoma. We have previously used microcell-mediated chromosome transfer (MMCT) to map an approximately 7.7 Mb colorectal cancer suppressor region (CRCSR) at 8p22-23.1. We have now taken a candidate gene approach to identify the putative tumor suppressor gene located within the CRCSR. CNOT7 encodes a subunit of the CCR4-Not transcription complex and is located at 8p22. We showed that CNOT7 is expressed in normal colonic mucosa and in colonic crypt cells, as well as in colorectal cell lines and primary tumors. We assembled a panel of 88 primary colorectal tumors comprising 20 MSI-high (high microsatellite instability), 19 MSI-low and 49 MSS (microsatellite stable) tumors for mutation analysis of the CNOT7 gene. Denaturing high-performance liquid chromatography (DHPLC) analysis of the entire coding region of the CNOT7 gene revealed only one somatic missense mutation in an MSS tumor. The rarity of somatic mutations in CNOT7, and its expression in primary colorectal tumors and cell lines, suggests that CNOT7 is not the target tumor suppressor gene in the 8p22-23.1 CRCSR.
MeSH term(s)	Carcinoma, Squamous Cell/genetics ; Chromatin Assembly Factor-1 ; Chromatography, High Pressure Liquid ; Chromosomal Proteins, Non-Histone ; Chromosome Deletion ; Chromosome Mapping ; Chromosomes, Human, Pair 8/genetics ; Colon/metabolism ; Colorectal Neoplasms/genetics ; DNA Mutational Analysis ; DNA Primers/chemistry ; DNA, Neoplasm/analysis ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Exons/genetics ; Gene Expression Regulation, Neoplastic ; Genes, Tumor Suppressor ; Humans ; Loss of Heterozygosity ; Microsatellite Repeats ; RNA, Neoplasm/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic ; Tumor Cells, Cultured
Chemical Substances	Chromatin Assembly Factor-1 ; Chromosomal Proteins, Non-Histone ; DNA Primers ; DNA, Neoplasm ; DNA-Binding Proteins ; RNA, Neoplasm
Language	English
Publishing date	2003-09-10
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218257-9
ISSN	1097-0215 ; 0020-7136
ISSN (online)	1097-0215
ISSN	0020-7136
DOI	10.1002/ijc.11264
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Zs.A 478: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: ENIGMA--evidence-based network for the interpretation of germline mutant alleles: an international initiative to evaluate risk and clinical significance associated with sequence variation in BRCA1 and BRCA2 genes.

Spurdle, Amanda B / Healey, Sue / Devereau, Andrew / Hogervorst, Frans B L / Monteiro, Alvaro N A / Nathanson, Katherine L / Radice, Paolo / Stoppa-Lyonnet, Dominique / Tavtigian, Sean / Wappenschmidt, Barbara / Couch, Fergus J / Goldgar, David E

Human mutation

2011 Volume 33, Issue 1, Page(s) 2–7

Abstract: As genetic testing for predisposition to human diseases has become an increasingly common practice in medicine, the need for clear interpretation of the test results is apparent. However, for many disease genes, including the breast cancer susceptibility ...

Abstract	As genetic testing for predisposition to human diseases has become an increasingly common practice in medicine, the need for clear interpretation of the test results is apparent. However, for many disease genes, including the breast cancer susceptibility genes BRCA1 and BRCA2, a significant fraction of tests results in the detection of a genetic variant for which disease association is not known. The finding of an "unclassified" variant (UV)/variant of uncertain significance (VUS) complicates genetic test reporting and counseling. As these variants are individually rare, a large collaboration of researchers and clinicians will facilitate studies to assess their association with cancer predisposition. It was with this in mind that the ENIGMA consortium (www.enigmaconsortium.org) was initiated in 2009. The membership is both international and interdisciplinary, and currently includes more than 100 research scientists and clinicians from 19 countries. Within ENIGMA, there are presently six working groups focused on the following topics: analysis, clinical, database, functional, tumor histopathology, and mRNA splicing. ENIGMA provides a mechanism to pool resources, exchange methods and data, and coordinately develop and apply algorithms for classification of variants in BRCA1 and BRCA2. It is envisaged that the research and clinical application of models developed by ENIGMA will be relevant to the interpretation of sequence variants in other disease genes.
MeSH term(s)	Algorithms ; Alleles ; Breast Neoplasms/diagnosis ; Breast Neoplasms/genetics ; Data Interpretation, Statistical ; Female ; Genes, BRCA1 ; Genes, BRCA2 ; Genetic Predisposition to Disease ; Genetic Testing/methods ; Genetic Testing/standards ; Genetic Variation ; Germ Cells ; Germ-Line Mutation ; Humans ; Organization and Administration ; Ovarian Neoplasms/diagnosis ; Ovarian Neoplasms/genetics ; Practice Guidelines as Topic ; RNA Splicing ; Risk Factors
Language	English
Publishing date	2011-11-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.21628
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Article ; Online: Splicing and multifactorial analysis of intronic BRCA1 and BRCA2 sequence variants identifies clinically significant splicing aberrations up to 12 nucleotides from the intron/exon boundary.

Whiley, Phillip J / Guidugli, Lucia / Walker, Logan C / Healey, Sue / Thompson, Bryony A / Lakhani, Sunil R / Da Silva, Leonard M / Tavtigian, Sean V / Goldgar, David E / Brown, Melissa A / Couch, Fergus J / Spurdle, Amanda B

Human mutation

2011 Volume 32, Issue 6, Page(s) 678–687

Abstract: Clinical management of breast cancer families is complicated by identification of BRCA1 and BRCA2 sequence alterations of unknown significance. Molecular assays evaluating the effect of intronic variants on native splicing can help determine their ... ...

Abstract	Clinical management of breast cancer families is complicated by identification of BRCA1 and BRCA2 sequence alterations of unknown significance. Molecular assays evaluating the effect of intronic variants on native splicing can help determine their clinical relevance. Twenty-six intronic BRCA1/2 variants ranging from the consensus dinucleotides in the splice acceptor or donor to 53 nucleotides into the intron were identified in multiple-case families. The effect of the variants on splicing was assessed using HSF matrices, MaxEntScan and NNsplice, followed by analysis of mRNA from lymphoblastoid cell lines. A total of 12 variants were associated with splicing aberrations predicted to result in production of truncated proteins, including a variant located 12 nucleotides into the intron. The posterior probability of pathogenicity was estimated using a multifactorial likelihood approach, and provided a pathogenic or likely pathogenic classification for seven of the 12 spliceogenic variants. The apparent disparity between experimental evidence and the multifactorial predictions is likely due to several factors, including a paucity of likelihood information and a nonspecific prior probability applied for intronic variants outside the consensus dinucleotides. Development of prior probabilities of pathogenicity incorporating bioinformatic prediction of splicing aberrations should improve identification of functionally relevant variants and enhance multifactorial likelihood analysis of intronic variants.
MeSH term(s)	Alternative Splicing ; BRCA1 Protein/genetics ; BRCA2 Protein/genetics ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Cell Line, Tumor ; Computational Biology ; Exons/genetics ; Female ; Genetic Variation ; Humans ; Introns/genetics ; Mutation ; RNA, Messenger/genetics
Chemical Substances	BRCA1 Protein ; BRCA2 Protein ; RNA, Messenger
Language	English
Publishing date	2011-04-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.21495
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Article: Gene expression profiling of formalin-fixed, paraffin-embedded familial breast tumours using the whole genome-DASL assay

Waddell, Nic / Cocciardi, Sibylle / Johnson, Julie / Healey, Sue / Marsh, Anna / Riley, Joan / Silva, Leonard da / Vargas, Ana Cristina / Reid, Lynne / Simpson, Peter T / Lakhani, Sunil R / Chenevix-Trench, Georgia

Journal of pathology. 2010 Aug., v. 221, no. 4

2010

Abstract: Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin-fixed, paraffin-embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumour banks. Once samples are ... ...

Abstract	Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin-fixed, paraffin-embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumour banks. Once samples are fixed in formalin, the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study, we have evaluated the ability of the whole genome DASL (cDNA-mediated Annealing, Selection, extension, and Ligation) assay from Illumina to perform transcriptomic analysis of archived breast tumour tissue in formalin-fixed, paraffin-embedded (FFPE) blocks. We profiled 76 familial breast tumours from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r² = 0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumour molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterization of many diseases. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Language	English
Dates of publication	2010-08
Size	p. 452-461.
Publishing place	John Wiley & Sons, Ltd.
Document type	Article
ZDB-ID	3119-7
ISSN	1096-9896 ; 0022-3417
ISSN (online)	1096-9896
ISSN	0022-3417
DOI	10.1002/path.2728
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Article ; Online: A genome wide linkage scan for dizygotic twinning in 525 families of mothers of dizygotic twins.

Painter, Jodie N / Willemsen, Gonneke / Nyholt, Dale / Hoekstra, Chantal / Duffy, David L / Henders, Anjali K / Wallace, Leanne / Healey, Sue / Cannon-Albright, Lisa A / Skolnick, Mark / Martin, Nicholas G / Boomsma, Dorret I / Montgomery, Grant W

Human reproduction (Oxford, England)

2010 Volume 25, Issue 6, Page(s) 1569–1580

Abstract: Background: The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning, we conducted a genome-wide linkage scan in 525 families using microsatellite and ...

Abstract	Background: The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning, we conducted a genome-wide linkage scan in 525 families using microsatellite and single nucleotide polymorphism marker panels. Methods and results: Non-parametric linkage analyses, including 523 families containing a total of 1115 mothers of DZ twins (MODZT) from Australia and New Zealand (ANZ) and The Netherlands (NL), produced four linkage peaks above the threshold for suggestive linkage, including a highly suggestive peak at the extreme telomeric end of chromosome 6 with an exponential logarithm of odds [(exp)LOD] score of 2.813 (P = 0.0002). Since the DZ twinning rate increases steeply with maternal age independent of genetic effects, we also investigated linkage including only families where at least one MODZT gave birth to her first set of twins before the age of 30. These analyses produced a maximum expLOD score of 2.718 (P = 0.0002), largely due to linkage signal from the ANZ cohort, however, ordered subset analyses indicated this result is most likely a chance finding in the combined dataset. Linkage analyses were also performed for two large DZ twinning families from the USA, one of which produced a peak on chromosome 2 in the region of two potential candidate genes. Sequencing of FSHR and FIGLA, along with INHBB in MODZTs from two large NL families with family specific linkage peaks directly over this gene, revealed a potentially functional variant in the 5' untranslated region of FSHR that segregated with the DZ twinning phenotype in the Utah family. Conclusion: Our data provide further evidence for complex inheritance of familial DZ twinning.
MeSH term(s)	Australia ; Family ; Female ; Genetic Linkage/genetics ; Genome-Wide Association Study ; Genotype ; Humans ; Male ; Maternal Age ; Netherlands ; New Zealand ; Phenotype ; Twins, Dizygotic/genetics
Language	English
Publishing date	2010-04-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	632776-x
ISSN	1460-2350 ; 0268-1161 ; 1477-741X
ISSN (online)	1460-2350
ISSN	0268-1161 ; 1477-741X
DOI	10.1093/humrep/deq084
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Article ; Online: Gene expression profiling of formalin-fixed, paraffin-embedded familial breast tumours using the whole genome-DASL assay.

Waddell, Nic / Cocciardi, Sibylle / Johnson, Julie / Healey, Sue / Marsh, Anna / Riley, Joan / da Silva, Leonard / Vargas, Ana Cristina / Reid, Lynne / Simpson, Peter T / Lakhani, Sunil R / Chenevix-Trench, Georgia

The Journal of pathology

2010 Volume 221, Issue 4, Page(s) 452–461

Abstract	Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin-fixed, paraffin-embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumour banks. Once samples are fixed in formalin, the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study, we have evaluated the ability of the whole genome DASL (cDNA-mediated Annealing, Selection, extension, and Ligation) assay from Illumina to perform transcriptomic analysis of archived breast tumour tissue in formalin-fixed, paraffin-embedded (FFPE) blocks. We profiled 76 familial breast tumours from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r(2) = 0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumour molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterization of many diseases.
MeSH term(s)	Ataxia Telangiectasia Mutated Proteins ; Breast Neoplasms/genetics ; Cell Cycle Proteins/genetics ; Cryopreservation ; DNA-Binding Proteins/genetics ; Female ; Formaldehyde ; Gene Expression Profiling/methods ; Genes, BRCA1 ; Genes, BRCA2 ; Genome ; Humans ; Neoplastic Syndromes, Hereditary/genetics ; Oligonucleotide Array Sequence Analysis/methods ; Paraffin Embedding ; Protein-Serine-Threonine Kinases/genetics ; RNA, Neoplasm/analysis ; Reproducibility of Results ; Retrospective Studies ; Tumor Suppressor Proteins/genetics
Chemical Substances	Cell Cycle Proteins ; DNA-Binding Proteins ; RNA, Neoplasm ; Tumor Suppressor Proteins ; Formaldehyde (1HG84L3525) ; ATM protein, human (EC 2.7.11.1) ; Ataxia Telangiectasia Mutated Proteins (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2010-08
Publishing country	England
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3119-7
ISSN	1096-9896 ; 0022-3417
ISSN (online)	1096-9896
ISSN	0022-3417
DOI	10.1002/path.2728
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