Understanding the Genetics of FTD a Guide for Patients and Their Families Acknowledgements
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Searching the Genomes of Inbred Mouse Strains for Incompatibilities That Reproductively Isolate Their Wild Relatives
Journal of Heredity 2007:98(2):115–122 ª The American Genetic Association. 2007. All rights reserved. doi:10.1093/jhered/esl064 For permissions, please email: [email protected]. Advance Access publication January 5, 2007 Searching the Genomes of Inbred Mouse Strains for Incompatibilities That Reproductively Isolate Their Wild Relatives BRET A. PAYSEUR AND MICHAEL PLACE From the Laboratory of Genetics, University of Wisconsin, Madison, WI 53706. Address correspondence to the author at the address above, or e-mail: [email protected]. Abstract Identification of the genes that underlie reproductive isolation provides important insights into the process of speciation. According to the Dobzhansky–Muller model, these genes suffer disrupted interactions in hybrids due to independent di- vergence in separate populations. In hybrid populations, natural selection acts to remove the deleterious heterospecific com- binations that cause these functional disruptions. When selection is strong, this process can maintain multilocus associations, primarily between conspecific alleles, providing a signature that can be used to locate incompatibilities. We applied this logic to populations of house mice that were formed by hybridization involving two species that show partial reproductive isolation, Mus domesticus and Mus musculus. Using molecular markers likely to be informative about species ancestry, we scanned the genomes of 1) classical inbred strains and 2) recombinant inbred lines for pairs of loci that showed extreme linkage disequi- libria. By using the same set of markers, we identified a list of locus pairs that displayed similar patterns in both scans. These genomic regions may contain genes that contribute to reproductive isolation between M. domesticus and M. -
Laboratory Testing for Her2 Status in Breast Cancer
Laboratory Testing for Her2 Status in Breast Cancer Katherine Geiersbach, M.D. Assistant Professor, Department of Pathology May 28, 2015 Overview • Clinical relevance of Her2 status for treatment of breast cancer • Standard approaches for determining Her2 status in breast cancer • Current concepts and controversies in Her2 testing 2 Who gets breast cancer? • Breast cancer is one of the most common malignancies to affect women • About 1 in 8 women will be diagnosed with breast cancer at some point in her lifetime • Most cases of breast cancer are sporadic, but a small percentage (5-10%) are related to a heritable gene mutation, most commonly BRCA1 or BRCA2 • Having a first degree relative with breast cancer increases a woman’s chance of developing breast cancer • Screening mammography is recommended for older women – US Preventive Services Task Force: Every 2 years starting at age 50 – American Cancer Society, others: Every 2 years starting at age 40 How is breast cancer treated? • Surgery: excision with or without sentinel lymph node biopsy – Breast conserving: lumpectomy, partial mastectomy – Mastectomy • Chemotherapy: before and/or after surgery • Radiation • Targeted therapies – Hormone therapy: Tamoxifen, aromatase inhibitors – Her2 targeted therapy for cancers with overexpression of the gene ERBB2, commonly called Her2 or Her2/neu • Treatment is based on testing for ER, PR, and Her2 status, as well as cancer grade and stage. 4 Her2 targeted therapy • Herceptin (trastuzumab) • Others: pertuzumab (Perjeta), T-DM1 (Kadcyla), and lapatinib (Tykerb) • Recent data shows that a combination of pertuzumab, trastuzumab, and docetaxel (PTD) improved progression free survival compared to patients who had only trastuzumab and docetaxel (TD)1,2 source: http://www.perjeta.com/hcp/moa 1. -
Duplications of 17P FTNW
Duplications of 17p rarechromo.org 17p duplications A 17p duplication means that the cells of the body have a small but variable amount of extra genetic material from one of their 46 chromosomes – chromosome 17. For healthy development, chromosomes should contain just the right amount of genetic material (DNA) – not too much and not too little. Like most other chromosome disorders, having an extra part of chromosome 17 may increase the risk of birth defects, developmental delay and learning (intellectual) disability. However, the problems vary and depend on what and how much genetic material is duplicated. Background on Chromosomes Chromosomes are structures which contain our DNA and are found in almost every cell of the body. Every chromosome contains thousands of genes which may be thought of as individual instruction booklets (or recipes) that contain all the genetic information telling the body how to develop, grow and function. Chromosomes (and genes) usually come in pairs with one member of each chromosome pair being inherited from each parent. Most cells of the human body have a total of 46 (23 pairs of) chromosomes. The egg and the sperm cells, however have 23 unpaired chromosomes, so that when the egg and sperm join together at conception, the chromosomes pair up and the number is restored to 46. Of these 46 chromosomes, two are the sex chromosomes that determine gender. Females have two X chromosomes and males have one X chromosome and one Y chromosome. The remaining 44 chromosomes are grouped in 22 pairs, numbered 1 to 22 approximately from the largest to the smallest. -
An In-Depth Analysis of the HER2 Amplicon and Chromosome 17
Rondón-Lagos et al. BMC Cancer 2014, 14:922 http://www.biomedcentral.com/1471-2407/14/922 RESEARCH ARTICLE Open Access Unraveling the chromosome 17 patterns of FISH in interphase nuclei: an in-depth analysis of the HER2 amplicon and chromosome 17 centromere by karyotyping, FISH and M-FISH in breast cancer cells Milena Rondón-Lagos1,4, Ludovica Verdun Di Cantogno2, Nelson Rangel1,4, Teresa Mele3, Sandra R Ramírez-Clavijo4, Giorgio Scagliotti3, Caterina Marchiò1,2*† and Anna Sapino1,2*† Abstract Background: In diagnostic pathology, HER2 status is determined in interphase nuclei by fluorescence in situ hybridization (FISH) with probes for the HER2 gene and for the chromosome 17 centromere (CEP17). The latter probe is used as a surrogate for chromosome 17 copies, however chromosome 17 (Chr17) is frequently rearranged. The frequency and type of specific structural Chr17 alterations in breast cancer have been studied by using comparative genomic hybridization and spectral karyotyping, but not fully detailed. Actually, balanced chromosome rearrangements (e.g. translocations or inversions) and low frequency mosaicisms are assessable on metaphases using G-banding karyotype and multicolor FISH (M-FISH) only. Methods: We sought to elucidate the CEP17 and HER2 FISH patterns of interphase nuclei by evaluating Chr17 rearrangements in metaphases of 9 breast cancer cell lines and a primary culture from a triple negative breast carcinoma by using G-banding, FISH and M-FISH. Results: Thirty-nine rearranged chromosomes containing a portion of Chr17 were observed. Chromosomes 8 and 11 were the most frequent partners of Chr17 translocations. The lowest frequency of Chr17 abnormalities was observed in the HER2-negative cell lines, while the highest was observed in the HER2-positive SKBR3 cells. -
BRCA1 and BRCA2 Genes and Their Relationship to Breast and Ovarian Cancer
Cancer Lab BRCA Teacher Background on DNA Bioinformatics Lab BRCA1 and BRCA2 Genes and Their Relationship to Breast and Ovarian Cancer Note: The Teacher Background Section is meant to provide information for the teacher about the topic and is tied very closely to the PowerPoint slide show. For greater understanding, the teacher may want to play the slide show as he/she reads the background section. For the students, the slide show can be used in its entirety or can be edited as necessary for a given class. What Are BRCA1 and BRCA2 and Where Are the Genes Located? BRCA1 and BRCA2 genes in humans code for proteins that work to suppress tumors. The gene names come from BReast CAncer genes 1 and 2. The official names of these genes are breast cancer 1, early onset and breast cancer 2, early onset. Everyone, male and female, has these genes which normally work to repair DNA and are involved in cell growth and cell division. The BRCA1 gene codes for the BRCA1 protein which regulates the activity of other genes and is involved in embryonic development during cell division. The BRCA2 gene codes for the BRCA2 protein which is thought to help regulate cytokinesis during cell division and to regulate telomere homeostasis. By helping repair DNA, BRCA1 and BRCA2 proteins are thought to work in tandem to ensure the stability of the DNA in the cell. The BRCA1 protein combines with BRCA2 and other proteins to mend breaks in the DNA caused by natural and medical exposures to radiation and other environmental exposures and by recombination when the chromosomes exchange genetic material when replicating prior to cell division. -
The Genomic Landscape of Centromeres in Cancers Anjan K
www.nature.com/scientificreports OPEN The Genomic Landscape of Centromeres in Cancers Anjan K. Saha 1,2,3, Mohamad Mourad3, Mark H. Kaplan3, Ilana Chefetz4, Sami N. Malek3, Ronald Buckanovich5, David M. Markovitz2,3,6,7 & Rafael Contreras-Galindo3,4 Received: 8 March 2019 Centromere genomics remain poorly characterized in cancer, due to technologic limitations in Accepted: 23 July 2019 sequencing and bioinformatics methodologies that make high-resolution delineation of centromeric Published: xx xx xxxx loci difcult to achieve. We here leverage a highly specifc and targeted rapid PCR methodology to quantitatively assess the genomic landscape of centromeres in cancer cell lines and primary tissue. PCR- based profling of centromeres revealed widespread heterogeneity of centromeric and pericentromeric sequences in cancer cells and tissues as compared to healthy counterparts. Quantitative reductions in centromeric core and pericentromeric markers (α-satellite units and HERV-K copies) were observed in neoplastic samples as compared to healthy counterparts. Subsequent phylogenetic analysis of a pericentromeric endogenous retrovirus amplifed by PCR revealed possible gene conversion events occurring at numerous pericentromeric loci in the setting of malignancy. Our fndings collectively represent a more comprehensive evaluation of centromere genetics in the setting of malignancy, providing valuable insight into the evolution and reshufing of centromeric sequences in cancer development and progression. Te centromere is essential to eukaryotic biology due to its critical role in genome inheritance1,2. Te nucleic acid sequences that dominate the human centromeric landscape are α-satellites, arrays of ~171 base-pair monomeric units arranged into higher-order arrays throughout the centromere of each chromosome3–103 1–3. -
17P13.3 Microdeletions
17p13.3 microdeletions rarechromo.org Sources 17p13.3 microdeletions The information in A 17p13.3 microdeletion is a rare disorder in which a small part this guide of the genetic material that makes up one of the body’s 46 encompasses details chromosomes is missing. Although the other chromosomes are on 28 separate intact, this small missing piece does increase the possibility of individuals with developmental delay and learning difficulties. However the 17p13.3 problems can vary and depend very much on what genetic microdeletions. This material is missing. information is drawn Chromosomes are made up mostly of DNA and are the partly from the structures in the nucleus of the body’s cells that carry genetic published medical information (known as genes), telling the body how to develop literature. There and function. Chromosomes usually come in pairs, one from were 21 published each parent, and are numbered 1 to 22 approximately from the cases in the medical largest to the smallest. In addition to these 44 chromosomes, literature with the each person has another pair of chromosomes, called the sex oldest person chromosomes. Girls have two Xs (XX), whereas boys have an X reported being 50 and a Y chromosome (XY). Each chromosome has a short (p) arm years old [Bruno (shown at the top in the diagram below) and a long (q) arm (the 2010]. The first- bottom part of the chromosome). named author and For healthy development, chromosomes should contain just the publication date are right amount of material – not too much and not too little. People given to allow you to with 17p13.3 microdeletions have one intact chromosome 17, but look for the the other is missing a tiny piece from the short arm which can abstracts or original affect their learning and physical development. -
Chromosome 17
Chromosome 17 Description Humans normally have 46 chromosomes in each cell, divided into 23 pairs. Two copies of chromosome 17, one copy inherited from each parent, form one of the pairs. Chromosome 17 spans about 83 million DNA building blocks (base pairs) and represents between 2.5 and 3 percent of the total DNA in cells. Identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to predict the number of genes on each chromosome, the estimated number of genes varies. Chromosome 17 likely contains 1, 100 to 1,200 genes that provide instructions for making proteins. These proteins perform a variety of different roles in the body. Health Conditions Related to Chromosomal Changes The following chromosomal conditions are associated with changes in the structure or number of copies of chromosome 17. 17q12 deletion syndrome 17q12 deletion syndrome is a condition that results from the deletion of a small piece of chromosome 17 in each cell. Signs and symptoms of 17q12 deletion syndrome can include abnormalities of the kidneys and urinary system, a form of diabetes called maturity-onset diabetes of the young type 5 (MODY5), delayed development, intellectual disability, and behavioral or psychiatric disorders. Some females with this chromosomal change have Mayer-Rokitansky-Küster-Hauser syndrome, which is characterized by underdevelopment or absence of the vagina and uterus. Features associated with 17q12 deletion syndrome vary widely, even among affected members of the same family. Most people with 17q12 deletion syndrome are missing about 1.4 million DNA building blocks (base pairs), also written as 1.4 megabases (Mb), on the long (q) arm of the chromosome at a position designated q12. -
Loss of Heterozygosity on Chromosomes 11 and 17 Are Markers of Recurrence in TCC of the Bladder
British Journal of Cancer (2001) 85(12), 1894–1899 © 2001 Cancer Research Campaign doi: 10.1054/ bjoc.2001.2159, available online at http://www.idealibrary.com on http://www.bjcancer.com Loss of heterozygosity on chromosomes 11 and 17 are markers of recurrence in TCC of the bladder J Edwards1, P Duncan1, JJ Going2, KM Grigor3, AD Watters1 and JMS Bartlett1 1University Department of Surgery and 2University Department of Pathology, Glasgow Royal Infirmary, Glasgow, G31 2ER; and 3University Department of Pathology, Edinburgh Royal Infirmary, Edinburgh, EH8 9AG, UK Summary Approximately 2/3 of patients diagnosed with superficial transitional cell carcinoma of the urinary bladder (TCC) will recur within 2 years. Loss of chromosome 9 and loss of heterozygosity (LOH) at 9q34 in index TCCs identify a subset of patients at high risk of recurrence. This study explores genetic alterations on chromosomes 4, 8, 11 and 17 as predictors of recurrence. A total of 109 carcinomas were investigated at 26 loci. DNA was extracted from microdissected archival normal/tumour tissue and was analysed for loss of heterozygosity (LOH). Fluorescent PCR was performed and genotyping carried out on a Perkin Elmer ABI377 sequencer. LOH of D11S490 or D17S928 was significantly more frequent in index carcinomas of patients who experienced recurrence compared to those with no recurrence (P = 0.004 and 0.019 respectively). These results suggest that loss of these regions is associated with recurrence of TCC. Further investigation is required to identify genes in these regions, -
The Mitotic Tensegrity Guardian Tau Protects Mammary Epithelia from Katanin-Like1-Induced Aneuploidy
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 33 Research Paper The mitotic tensegrity guardian tau protects mammary epithelia from katanin-like1-induced aneuploidy Haruka Sudo1,2, Kazunori Nakajima2 1Department of Biochemistry, The Nippon Dental University School of Life Dentistry at Tokyo, 1-9-20 Fujimi, Chiyoda-ku, Tokyo 102-8159, Japan 2Department of Anatomy, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan Correspondence to: Haruka Sudo, email: [email protected] Keywords: breast cancer, chromosome instability, microtubule severing, mitotic spindle, tau Received: January 17, 2016 Accepted: June 16, 2016 Published: July 20, 2016 ABSTRACT The microtubule associated-protein tau has been identified as an effective positive prognostic indicator in breast cancer. To explore the physiological function of tau in early carcinogenesis, endogenous tau was knocked down in primary cultured human mammary epithelial cells. This resulted in chromosome-bridging during anaphase followed by micronucleation, both of which were suppressed by a further katanin- like1 knockdown. We also detected that the exogenously expressed katanin-like1 induction of cellular transformation is prevented by exogenous tau in rat fibroblasts. The mutant katanin-like1 (L123V) identified in breast cancer showed an increase in this transformation capacity as well as microtubule severing activity resistant to tau. The tau knockdown resulted in a loss of the kinetochore fibers on which tau is normally localized. This physical fragility was also observed in isolated tau- knockdown mitotic spindles, supporting the relevance of microtubule damage to the onset of transformation. The karyotyping of tau-knockdown cells showed increased frequency of loss of one X chromosome, further suggesting the involvement of tau in breast tumorigenesis. -
Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics
cells Review Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics Syed Farhan Ahmad 1,2, Worapong Singchat 1,2, Maryam Jehangir 1,3, Aorarat Suntronpong 1,2, Thitipong Panthum 1,2, Suchinda Malaivijitnond 4,5 and Kornsorn Srikulnath 1,2,4,6,7,* 1 Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; [email protected] (S.F.A.); [email protected] (W.S.); [email protected] (M.J.); [email protected] (A.S.); [email protected] (T.P.) 2 Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand 3 Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil 4 National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand; [email protected] 5 Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand 6 Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand 7 Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand * Correspondence: [email protected] Received: 27 October 2020; Accepted: 16 December 2020; Published: 18 December 2020 Abstract: A substantial portion of the primate genome is composed of non-coding regions, so-called “dark matter”, which includes an abundance of tandemly repeated sequences called satellite DNA. Collectively known as the satellitome, this genomic component offers exciting evolutionary insights into aspects of primate genome biology that raise new questions and challenge existing paradigms. -
Translocation and Amplification of an X-Chromosome DNA Repeat in Inbred Strains of Mice
Volume 15 Number 11 1987 Nucleic Acids Research Translocation and amplification of an X-chromosome DNA repeat in inbred strains of mice Christine M.Disteche, Shawna L.Gandy and David A.Adler Department of Pathology SM-30, University of Washington, Seattle, WA 98195, USA Received March 19, 1987; Revised and Accepted May 13, 1987 ABSTRACT A 9-kb repetitive DNA fragment (70-38) located near the centromere of the mouse X chromosome is amplified and translocated to an autosome in different inbred strains of mice. In situ hybridization and hybrid cell studies showed that probe 70-38 is located only on the X chromosome in mouse strains A/J, AKR/J, BALB/cJ, CBA/J, C3H/HeJ, C57BL/6J, DBA/2J and SWR/J. However, in four other mouse strains the DNA sequence is found near the centromere of an autosome in addition to the X chromosome. This autosome differs among the mouse strains (chromosome 11 in C57BL/lOJ or ScSn, chromosome 13 in NZB/BlNJ and chromosome 17 in SJL/J and PO). In those strains where the repeated sequence is located on an autosome, it has been amplified to about 100 copies. Restriction enzyme digestion patterns suggest a common structure for 70-38 sequences in the different strains. The changes in copy number, restriction enzyme digestion patterns, and chromosomal location of 70-38 reflect a rapid genomic evolution in inbred mouse strains. INTRODUCTION Repeated and satellite DNA sequences represent a large proportion of the eukaryotic genome and are likely to play an important role in chromosomal organization and function.