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Bornstein AT, McLoughlin MH, Aguilar J, Wong WSW, Solomon BD. Tracking medical genetic literature through machine learning. Mol Genet Metab 2016; 118:255-8. [PMID: 27268407 DOI: 10.1016/j.ymgme.2016.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 11/17/2022]
Abstract
There has been remarkable progress in identifying the causes of genetic conditions as well as understanding how changes in specific genes cause disease. Though difficult (and often superficial) to parse, an interesting tension involves emphasis on basic research aimed to dissect normal and abnormal biology versus more clearly clinical and therapeutic investigations. To examine one facet of this question and to better understand progress in Mendelian-related research, we developed an algorithm that classifies medical literature into three categories (Basic, Clinical, and Management) and conducted a retrospective analysis. We built a supervised machine learning classification model using the Azure Machine Learning (ML) Platform and analyzed the literature (1970-2014) from NCBI's Entrez Gene2Pubmed Database (http://www.ncbi.nlm.nih.gov/gene) using genes from the NHGRI's Clinical Genomics Database (http://research.nhgri.nih.gov/CGD/). We applied our model to 376,738 articles: 288,639 (76.6%) were classified as Basic, 54,178 (14.4%) as Clinical, and 24,569 (6.5%) as Management. The average classification accuracy was 92.2%. The rate of Clinical publication was significantly higher than Basic or Management. The rate of publication of article types differed significantly when divided into key eras: Human Genome Project (HGP) planning phase (1984-1990); HGP launch (1990) to publication (2001); following HGP completion to the "Next Generation" advent (2009); the era following 2009. In conclusion, in addition to the findings regarding the pace and focus of genetic progress, our algorithm produced a database that can be used in a variety of contexts including automating the identification of management-related literature.
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Affiliation(s)
| | | | | | - Wendy S W Wong
- Inova Translational Medicine Institute, Falls Church, VA 22042, USA
| | - Benjamin D Solomon
- Inova Translational Medicine Institute, Falls Church, VA 22042, USA; Inova Children's Hospital, Falls Church, VA 22042, USA; Department of Pediatrics, Virginia Commonwealth University, Richmond, VA 23298, USA.
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Kargieman L, Herrera E, Baez S, García AM, Dottori M, Gelormini C, Manes F, Gershanik O, Ibáñez A. Motor-Language Coupling in Huntington's Disease Families. Front Aging Neurosci 2014; 6:122. [PMID: 24971062 PMCID: PMC4054328 DOI: 10.3389/fnagi.2014.00122] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 05/27/2014] [Indexed: 11/24/2022] Open
Abstract
Traditionally, Huntington’s disease (HD) has been known as a movement disorder, characterized by motor, psychiatric, and cognitive impairments. Recent studies have shown that motor and action–language processes are neurally associated. The cognitive mechanisms underlying this interaction have been investigated through the action compatibility effect (ACE) paradigm, which induces a contextual coupling of ongoing motor actions and verbal processing. The present study is the first to use the ACE paradigm to evaluate action–word processing in HD patients (HDP) and their families. Specifically, we tested three groups: HDP, healthy first-degree relatives (HDR), and non-relative healthy controls. The results showed that ACE was abolished in HDP as well as HDR, but not in controls. Furthermore, we found that the processing deficits were primarily linguistic, given that they did not correlate executive function measurements. Our overall results underscore the role of cortico-basal ganglia circuits in action–word processing and indicate that the ACE task is a sensitive and robust early biomarker of HD and familial vulnerability.
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Affiliation(s)
- Lucila Kargieman
- Laboratory of Experimental Psychology and Neuroscience (LPEN), Institute of Cognitive Neurology (INECO), Favaloro University , Buenos Aires , Argentina ; National Scientific and Technical Research Council (CONICET) , Buenos Aires , Argentina ; UDP-INECO Foundation Core on Neuroscience (UIFCoN), Diego Portales University , Santiago , Chile
| | - Eduar Herrera
- Laboratory of Experimental Psychology and Neuroscience (LPEN), Institute of Cognitive Neurology (INECO), Favaloro University , Buenos Aires , Argentina ; National Scientific and Technical Research Council (CONICET) , Buenos Aires , Argentina ; Universidad Autónoma del Caribe , Barranquilla , Colombia
| | - Sandra Baez
- Laboratory of Experimental Psychology and Neuroscience (LPEN), Institute of Cognitive Neurology (INECO), Favaloro University , Buenos Aires , Argentina ; National Scientific and Technical Research Council (CONICET) , Buenos Aires , Argentina ; UDP-INECO Foundation Core on Neuroscience (UIFCoN), Diego Portales University , Santiago , Chile
| | - Adolfo M García
- Laboratory of Experimental Psychology and Neuroscience (LPEN), Institute of Cognitive Neurology (INECO), Favaloro University , Buenos Aires , Argentina ; National Scientific and Technical Research Council (CONICET) , Buenos Aires , Argentina ; UDP-INECO Foundation Core on Neuroscience (UIFCoN), Diego Portales University , Santiago , Chile ; School of Languages, National University of Córdoba (UNC) , Córdoba , Argentina
| | - Martin Dottori
- Laboratory of Experimental Psychology and Neuroscience (LPEN), Institute of Cognitive Neurology (INECO), Favaloro University , Buenos Aires , Argentina
| | - Carlos Gelormini
- Laboratory of Experimental Psychology and Neuroscience (LPEN), Institute of Cognitive Neurology (INECO), Favaloro University , Buenos Aires , Argentina
| | - Facundo Manes
- Laboratory of Experimental Psychology and Neuroscience (LPEN), Institute of Cognitive Neurology (INECO), Favaloro University , Buenos Aires , Argentina ; National Scientific and Technical Research Council (CONICET) , Buenos Aires , Argentina ; Australian Research Council (ARC) Centre of Excellence in Cognition and its Disorders , Sydney, NSW , Australia
| | - Oscar Gershanik
- Laboratory of Experimental Psychology and Neuroscience (LPEN), Institute of Cognitive Neurology (INECO), Favaloro University , Buenos Aires , Argentina ; National Scientific and Technical Research Council (CONICET) , Buenos Aires , Argentina
| | - Agustín Ibáñez
- Laboratory of Experimental Psychology and Neuroscience (LPEN), Institute of Cognitive Neurology (INECO), Favaloro University , Buenos Aires , Argentina ; National Scientific and Technical Research Council (CONICET) , Buenos Aires , Argentina ; UDP-INECO Foundation Core on Neuroscience (UIFCoN), Diego Portales University , Santiago , Chile ; Universidad Autónoma del Caribe , Barranquilla , Colombia
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Ross CA, Margolis RL, Rosenblatt A, Ranen NG, Becher MW, Aylward E. Huntington disease and the related disorder, dentatorubral-pallidoluysian atrophy (DRPLA). Medicine (Baltimore) 1997; 76:305-38. [PMID: 9352736 DOI: 10.1097/00005792-199709000-00001] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- C A Ross
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA
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Duyao M, Ambrose C, Myers R, Novelletto A, Persichetti F, Frontali M, Folstein S, Ross C, Franz M, Abbott M. Trinucleotide repeat length instability and age of onset in Huntington's disease. Nat Genet 1993; 4:387-92. [PMID: 8401587 DOI: 10.1038/ng0893-387] [Citation(s) in RCA: 715] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The initial observation of an expanded and unstable trinucleotide repeat in the Huntington's disease gene has now been confirmed and extended in 150 independent Huntington's disease families. HD chromosomes contained 37-86 repeat units, whereas normal chromosomes displayed 11-34 repeats. The HD repeat length was inversely correlated with the age of onset of the disorder. The HD repeat was unstable in more than 80% of meiotic transmissions showing both increases and decreases in size with the largest increases occurring in paternal transmissions. The targeting of spermatogenesis as a particular source of repeat instability is reflected in the repeat distribution of HD sperm DNA. The analysis of the length and instability of individual repeats in members of these families has profound implications for presymptomatic diagnosis.
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Affiliation(s)
- M Duyao
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown 02129
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Affiliation(s)
- J F Gusella
- Department of Genetics, Harvard Medical School, Cambridge, Massachusetts 02138
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Strobel SA, Doucette-Stamm LA, Riba L, Housman DE, Dervan PB. Site-specific cleavage of human chromosome 4 mediated by triple-helix formation. Science 1991; 254:1639-42. [PMID: 1836279 DOI: 10.1126/science.1836279] [Citation(s) in RCA: 137] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Direct physical isolation of specific DNA segments from the human genome is a necessary goal in human genetics. For testing whether triple-helix mediated enzymatic cleavage can liberate a specific segment of a human chromosome, the tip of human chromosome 4, which contains the entire candidate region for the Huntington's disease gene, was chosen as a target. A 16-base pyrimidine oligodeoxyribonucleotide was able to locate a 16-base pair purine target site within more than 10 gigabase pairs of genomic DNA and mediate the exact enzymatic cleavage at that site in more than 80 percent yield. The recognition motif is sufficiently generalizable that most cosmids should contain a sequence targetable by triple-helix formation. This method may facilitate the orchestrated dissection of human chromosomes from normal and affected individuals into megabase sized fragments and facilitate the isolation of candidate gene loci.
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Affiliation(s)
- S A Strobel
- Arnold and Mabel Beckman Laboratories of Chemical Synthesis, California Institute of Technology, Pasadena 91125
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Blanton SH, Heckenlively JR, Cottingham AW, Friedman J, Sadler LA, Wagner M, Friedman LH, Daiger SP. Linkage mapping of autosomal dominant retinitis pigmentosa (RP1) to the pericentric region of human chromosome 8. Genomics 1991; 11:857-69. [PMID: 1783394 DOI: 10.1016/0888-7543(91)90008-3] [Citation(s) in RCA: 129] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Linkage mapping in a large, seven-generation family with type 2 autosomal dominant retinitis pigmentosa (ADRP) demonstrates linkage between the disease locus (RP1) and DNA markers on the short arm of human chromosome 8. Five markers were most informative for mapping ADRP in this family using two-point linkage analysis. The markers, their maximum lod scores, and recombination distances were ANK1 (ankyrin)--2.0 at 16%; D8S5 (TL11)--5.3 at 17%; D8S87 [a(CA)n repeat]--7.2 at 14%; LPL (lipoprotein lipase)--1.5 at 26%; and PLAT (plasminigen activator, tissue)--10.6 at 7%. Multipoint linkage analysis, using a simplified pedigree structure for the family (which contains 192 individuals and two inbreeding loops), gave a maximum lod score of 12.2 for RP1 at a distance 8.1 cM proximal to PLAT in the pericentric region of the chromosome. Based on linkage data from the CEPH (Paris) reference families and physical mapping information from a somatic cell hybrid panel of chromosome 8 fragments, the most likely order for four of these five loci and the diseases locus is 8pter-LPL-D8S5-D8S87-PLAT-RP1. (The precise location of ANK1 relative to PLAT in this map is not established). The most likely location for RP1 is in the pericentric region of the chromosome. Recently, several families with ADRP with tight linkage to the rhodopsin locus at 3q21-q24 were reported and a number of specific rhodopsin mutations in families with ADRP have since been reported. In other ADRP families, including the one in this study, linkage to rhodopsin has been excluded. Thus mutations at two different loci, at least, have been shown to cause ADRP. There is no remarkable clinical disparity in the expression of disease caused by these different loci.
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Affiliation(s)
- S H Blanton
- Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston 77030
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Greenberg LJ, Martell RW, Theilman J, Hayden MR, Joubert J. Genetic linkage between Huntington disease and the D4S10 locus in South African families: further evidence against non-allelic heterogeneity. Hum Genet 1991; 87:701-8. [PMID: 1834541 DOI: 10.1007/bf00201729] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A study of genetic linkage between Huntington disease (HD) and the D4S10 locus (G8) has been undertaken in 10 South African (SA) families originating from the black, white and mixed acestry population groups. Allele frequencies at the D4S10 locus have been established in the non-Caucasoid population groups. There are significant differences in the allele frequencies at the D4S10 locus between the various SA populations. Clearly, information about population-specific frequencies for all polymorphisms is essential prior to the implementation of predictive testing in different population groups. Linkage has been demonstrated within this mixed group of HD families in SA using the HindIII, EcoRI and MspI polymorphisms, detected by G8. A maximum lod score of 8.14 at a recombination fraction of 0.00 (confidence limit 0-0.058) has been calculated using a combined haplotype of the HindIII and MspI polymorphisms. Taking into account the diverse ethnic backgrounds of the different SA population groups in this investigation, the data obtained from the study provide further evidence that there is probably only a single HD locus.
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Affiliation(s)
- L J Greenberg
- Department of Human Genetics, University of Cape Town Medical School, Observatory, South Africa
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Ridley RM, Frith CD, Farrer LA, Conneally PM. Patterns of inheritance of the symptoms of Huntington's disease suggestive of an effect of genomic imprinting. J Med Genet 1991; 28:224-31. [PMID: 1830339 PMCID: PMC1016822 DOI: 10.1136/jmg.28.4.224] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The interaction of symptomatology (rigidity/chorea) in Huntington's disease (HD) with age of onset (AO) was examined using data from the Research Roster for Huntington's Disease Patients and Families. It was shown that AO varies between families and between paternal and maternal transmission and that rigidity is associated specifically with very early onset, major anticipation, paternal transmission, and young parental AO. It is proposed that AO depends on the state of methylation of the HD locus, which varies as a familial trait, and as a consequence of 'genomic imprinting' determined by parental transmission. Young familial AO and paternal imprinting interact to produce, occasionally, a major change in gene expression, that is, the early onset/rigid variant.
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Affiliation(s)
- R M Ridley
- Division of Psychiatry, Clinical Research Centre, Northwick Park Hospital, Harrow, Middlesex
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Abstract
This article presents data on the large Huntington's disease (HD) family of Tasmania. Nine generations have been traced, starting with the father of the woman who brought the disease to the State. From that woman, six lines have living affected descendants. There are 765 living descendants who are "at risk" of HD. The numbers of affected males and females are equal. Affected members of the family have a mean age of onset of HD of 48.6 years and a mean age of death of 61.8 years. Affected members are at least as fertile as members of the general population. Late-onset disease is associated with significantly greater fertility (in men more so than women) compared with that of unaffected siblings of the same sex. Men with late-onset disease had a significantly older mean age of reproduction than that of their unaffected male siblings, and they had significantly more offspring than the number calculated for the general population of Tasmania. Unaffected siblings produced fewer offspring than in the general population.
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Affiliation(s)
- S A Pridmore
- Department of Psychiatry, University of Tasmania Clinical School, Hobart
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Abstract
Various aspects of the age of onset of Huntington's disease (HD) were studied using extensive Tasmanian data. The mean age of onset of those born before 1930 was determined. For the total Tasmanian population of HD sufferers, this was 48.3 years. This finding has clinical implications because the most dangerous period for "at risk" individuals is frequently stated to be between 20 and 45 years. The range of age of onset for one very large Tasmanian family (the "Brothers family") is 53 years, from the second to the seventh decade. There were no juvenile-onset cases (onset before 20 years of age) in patients born in Tasmania before 1930. Three juvenile cases have occurred in those born since 1930. Support was found for the observation of paternal transmission in juvenile-onset HD. No support was found for the observation of maternal transmission in late-onset disease (50 years and beyond).
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Affiliation(s)
- S A Pridmore
- Department of Psychiatry, University of Tasmania, Hobart
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Abstract
The records of all Huntington's disease affected individuals born in Tasmania were examined. An age of birth exclusion criterion (only those born before 1928 were accepted) removed some bias in the determination of duration of illness and age of death. The mean age of death was at least 62.9 years. This is the oldest mean age of death reported for any geographical region. The sex of the affected individual and the sex of the transmitting parent did not significantly influence the mean age of death. The children of affected women lived to a greater age than theri mothers and the children of affected men died at a younger age than their fathers, but statistical significance was not achieved. The duration of the disease was 14.8 years.
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Affiliation(s)
- S A Pridmore
- Department of Psychiatry, University of Tasmania, Hobart
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Allen ND, Norris ML, Surani MA. Epigenetic control of transgene expression and imprinting by genotype-specific modifiers. Cell 1990; 61:853-61. [PMID: 2111735 DOI: 10.1016/0092-8674(90)90195-k] [Citation(s) in RCA: 195] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Expression and DNA methylation of the transgene locus TKZ751 are controlled by genotype-specific modifier genes. The DBA/2 and 129 genetic backgrounds enhanced expression, while the BALB/c background suppressed expression, but only following maternal inheritance of the BALB/c modifier. Epigenetic modification of the transgene locus was cumulative over successive generations, which in BALB/c mice resulted in an irreversible methylation after three consecutive germline passages. Therefore, at the TKZ751 locus the germline fails to reverse previously acquired epigenetic modifications, a process that is usually essential to restore the genomic totipotency. Hence the genotype-specific modifier genes regulate penetrance and expressivity as well as parental imprinting of the TKZ751 locus through epigenetic modification.
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Affiliation(s)
- N D Allen
- Department of Molecular Embryology, AFRC Institute of Animal Physiology and Genetics Research, Babraham, Cambridge, England
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Abstract
In a considerable number of genetic disorders in the human, the phenotypic expression of the disease can depend on maternal or paternal inheritance of the mutation. It is suggested that genomic imprinting, an epigenetic process that marks maternal and paternal chromosomes in mammals, is involved in such parental effects.
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Affiliation(s)
- R Kurlan
- Department of Neurology, University of Rochester School of Medicine, New York 14642
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Zweig RM, Koven SJ, Hedreen JC, Maestri NE, Kazazian HH, Folstein SE. Linkage to the Huntington's disease locus in a family with unusual clinical and pathological features. Ann Neurol 1989; 26:78-84. [PMID: 2528319 DOI: 10.1002/ana.410260112] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We used the anonymous DNA probe, D4S10 (G8), known to be linked to the Huntington's disease (HD) locus, to confirm inheritance at that locus in a family in whom most affected individuals had atypical clinical and pathological features. Their clinical features were similar to the Westphal variant (usually seen in juvenile-onset HD) but they had onset in adult life, and in contrast to juvenile-onset HD, their course of illness was prolonged. Most family members had been repeatedly misdiagnosed during life because of the absence of chorea and prominence of long-tract signs. In 2 patients who died, neuropathological examination at autopsy revealed prominent involvement of brainstem and spinal cord structures, and in 1, mild neostriatal atrophy relative to duration of the disease. The study demonstrates the usefulness of genetic linkage analysis as a diagnostic tool in families with atypical forms of HD. This method allows study of phenotypic variations that can be inherited at or near the HD locus and implies either multiple alleles at the locus gene, modifiers of a single allele, or another locus in the same region causing a dominantly inherited neurodegenerative disease.
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Affiliation(s)
- R M Zweig
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
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Pritchard CA, Casher D, Uglum E, Cox DR, Myers RM. Isolation and field-inversion gel electrophoresis analysis of DNA markers located close to the Huntington disease gene. Genomics 1989; 4:408-18. [PMID: 2523854 DOI: 10.1016/0888-7543(89)90348-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A radiation-induced hybrid cell line containing 10-20 million base pairs of DNA derived from the terminal part of human 4p16 in a background of hamster chromosomes has been used to construct a genomic library highly enriched for human sequences located close to the Huntington disease (HD) gene. Recombinant phage containing human inserts were isolated from this library and used as hybridization probes against two other radiation hybrids containing human fragments with chromosomal breaks in 4p16 and against a human-hamster somatic cell hybrid that retains only the 4p15-4pter part of chromosome 4. Of 121 human phage tested, 6 were mapped distal to the HD-linked D4S10 locus. Since the HD gene is located between D4S10 and the 4p telomere, all of these sequences are likely to be closer to HD than D4S10, and any one of them may be a distal flanking marker for the disease locus. Long-range restriction map analysis performed with a field-inversion gel system shows that the six new loci are distributed in different places within 4p16. Although it is not possible to establish an order for the six sequences with the FIGE data, the results demonstrate that the region detected by these probes must span at least 2000 kb of DNA.
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Affiliation(s)
- C A Pritchard
- Department of Physiology, University of California, San Francisco 94143
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Holloway S, Millan FA, Curtis A, Mennie M, Brock DJ. Genetic linkage between Huntington's disease and D4S10 (G8) in Scottish families. Clin Genet 1989; 35:133-8. [PMID: 2524298 DOI: 10.1111/j.1399-0004.1989.tb02918.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic linkage between Huntington's disease (HD) and polymorphic DNA markers at the D4S10 locus has been investigated in 16 Scottish families. A maximum lod score of 3.499 at a recombination fraction of 0.07 was found, with 95% confidence limits of 0.02 and 0.22. Only one obvious recombinant was detected, and the wide confidence limits probably reflect the large number of unaffected individuals whose risk could only be estimated empirically.
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Affiliation(s)
- S Holloway
- Human Genetics Unit, University of Edinburgh, Western General Hospital, Scotland, UK
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Abstract
In the past 10 years considerable progress has been made in the diagnosis of hereditary disorders at the DNA level. Many monogenic disorders can now be examined at the gene level; such examination has led to a better understanding of the molecular basis of these disorders and made carrier detection and prenatal diagnosis possible. Each year, more and more monogenic disorders can be added to the list of diseases that can be diagnosed by DNA analysis. Future research will be devoted to the identification of genes responsible for other known monogenic hereditary disorders, the elucidation of the molecular lesion associated with chromosomal abnormalities, and the characterization of the genes and gene defects involved in the common multifactorial diseases. The goal of diagnosis is the identification of the genetic defect in affected patients, persons destined to be affected, and carriers.
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Affiliation(s)
- S E Antonarakis
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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Schiffmann SN, Vanderhaeghen JJ. Increase of substance P and met-enkephalin in a severely atrophied striatum without clinical expression of chorea. Neurochem Int 1989; 14:175-83. [DOI: 10.1016/0197-0186(89)90119-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/1988] [Indexed: 10/27/2022]
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Reik W. Genomic imprinting: a possible mechanism for the parental origin effect in Huntington's chorea. J Med Genet 1988; 25:805-8. [PMID: 2976840 PMCID: PMC1051607 DOI: 10.1136/jmg.25.12.805] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Huntington's disease (HD) is an autosomal dominant condition with almost complete penetrance. The age of onset of the symptoms, however, is variable and depends on the parental origin of the gene. A high proportion of early onset cases inherit the HD gene from their father, whereas a considerable proportion of late onset cases inherit the gene from their mother. Modification of the HD gene by maternally inherited extrachromosomal factors has been invoked to account for the parental origin effect. Recent experimental evidence suggests genomic imprinting as an alternative mechanism, by which the gene itself becomes modified in a different way depending on whether it is passed through the maternal or the paternal germline. This modification may involve methylation of DNA and could result in earlier or higher level expression of the gene when it is transmitted by the father.
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Affiliation(s)
- W Reik
- Department of Molecular Embryology, Institute of Animal Physiology and Genetics Research, Cambridge
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Farrer LA, Myers RH, Cupples LA, Conneally PM. Considerations in using linkage analysis as a presymptomatic test for Huntington's disease. J Med Genet 1988; 25:577-88. [PMID: 2903248 PMCID: PMC1051534 DOI: 10.1136/jmg.25.9.577] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The polymorphic locus D4S10 that is genetically linked to the locus for Huntington's disease (HD) has made possible a presymptomatic test for those at risk. Because the symptoms of this progressively debilitating and fatal illness are not usually manifest until adulthood, the outcome of the test will influence major decisions about career, marriage, and procreation. Several differential diagnoses must be considered before using the test if HD is not confirmed in at least one family member. Review of a large number of pedigrees has shown that 40% of persons at risk do not have appropriate family structure for a linkage test. Furthermore, uncooperative or inaccessible relatives may make this test infeasible for many others who wish to be tested. Linkage phase, which must be known in the affected parent for an informative test, can be determined using one or more of 12 probe-enzyme combinations for D4S10. Although the polymorphism information content (PIC) value for any one RFLP is less than 40%, the PIC value for the haplotype of the two G8 HindIII, pK083 EcoRI, and R7 BglII RFLPs is greater than 88%. We have developed a scheme to incorporate linkage data and age at onset information adjusted for censored observations, sex of affected parent, and familial correlation for age at onset, using the computer program MLINK for calculation of risk of having HD. Simulated experiments showed that proper age at onset adjustment is crucial to the calculation of the probability of risk. A formal presymptomatic testing protocol, including pre- and post-test counselling, psychological testing, and paternity testing is recommended. Many of these considerations are illustrated in several actual test cases.
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Affiliation(s)
- L A Farrer
- Department of Neurology, Boston University School of Medicine, MA 02118
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Ridley RM, Frith CD, Crow TJ, Conneally PM. Anticipation in Huntington's disease is inherited through the male line but may originate in the female. J Med Genet 1988; 25:589-95. [PMID: 2972838 PMCID: PMC1051535 DOI: 10.1136/jmg.25.9.589] [Citation(s) in RCA: 113] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Data from the US National Huntington's Disease Roster have been analysed in terms of the difference in age of onset (AO) between affected parents and affected offspring, that is, in terms of 'anticipation'. While mean AO in offspring of affected mothers did not differ greatly from AO in their mothers, the distribution of AO in the offspring of affected fathers falls into two groups, the larger group showing an AO only slightly younger than their affected fathers and a small group whose AO was, on average, 24 years younger than their affected fathers. Analysis of the grandparental origin of the Huntington allele suggests that while propensity to anticipation is heritable for a number of generations through the male line, it originates at the time of differentiation of the germ line of a male who acquires the Huntington allele from his mother. It is suggested that major anticipation indicates an epigenetic change in methylation of the nucleic acid of the genome, which is imposed in the course of the 'genomic imprinting', that is, in the mechanism by which the parental origin of alleles is indicated.
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Affiliation(s)
- R M Ridley
- Division of Psychiatry, Clinical Research Centre, Harrow, Middlesex
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26
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Abstract
Huntington disease is an autosomal dominant disorder that usually begins in mid-life and is characterized by progressive choreiform movements and dementia. Approximately 5% of patients develop symptoms prior to 14 years of age. In most juvenile cases, the gene is transmitted from the father. In children the clinical course is marked by mental deterioration or behavioral abnormalities, gait disturbances usually the consequence of rigidity, cerebellar signs, and seizures. The pathologic findings are highlighted by atrophy of the caudate. Atrophy also is observed on brain imaging, while positron emission tomography demonstrates marked caudate hypometabolism which antedates the appearance of the clinical disease. Cell death in the striatum primarily affects medium and small GABA-containing neurons, representing the striatal output projections. Somatostatin-containing neurons and cholinergic neurons are spared. The gene for Huntington disease has been localized in close proximity to the tip of the short arm of chromosome 4. The gene product and the manner by which it induces selective cell death is still unknown but should become evident in the near future.
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Affiliation(s)
- J H Menkes
- Department of Neurology and Pediatrics, Reed Neurologic Research Center, Los Angeles, CA 90024-1769
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27
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Moss RJ, Mastri AR, Schut LJ. The coexistence and differentiation of late onset Huntington's disease and Alzheimer's disease. A case report and review of the literature. J Am Geriatr Soc 1988; 36:237-41. [PMID: 2963060 DOI: 10.1111/j.1532-5415.1988.tb01807.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The case report presented is clinically compatible with late onset HD. The diagnosis was initially obscured by a lack of family history due to the early death of both parents and siblings. The presence of symptoms at the age of 59 in one offspring is consistent with the intrafamilial transmission of late onset HD disease. The early neuropsychometric data were consistent with the cognitive changes of HD, particularly with the loss of higher cognitive functions, memory and the relative decline in the performance IQ with the preservation of language skills. The psychiatric symptoms of emotional lability and apathy were also congruent with the diagnosis of HD. The atypical features of this patient's course, including progressively severe dementia, seizures and rigidity, may have provided clinical clues to the coexistence of both AD and HD. The absence of caudate atrophy on serial CT scans in this patient, although inconsistent with the gross findings reported on postmortem exam, perhaps could be explained by the 3 1/2-year interval between the last CT scan and death. Further, it has been noted previously that pathological changes tend to lag behind the clinical manifestations of the disease. The pathologic findings on autopsy were confirmatory for the presence of both AD and HD in this patient. Genetic counseling for this family is now most appropriate.
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Affiliation(s)
- R J Moss
- Veterans Administration Medical Center, Geriatric Research, Education and Clinical Center, Minneapolis, MN 55417
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28
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Quarrell OW, Youngman S, Sarfarazi M, Harper PS. Absence of close linkage between benign hereditary chorea and the locus D4S10 (probe G8). J Med Genet 1988; 25:191-4. [PMID: 2895189 PMCID: PMC1015485 DOI: 10.1136/jmg.25.3.191] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A genetic linkage study between benign hereditary chorea and the locus D4S10 using the DNA probe G8 has shown two recombinations in five small families. There were negative lod scores at recombination fractions that show conclusive evidence of linkage in 16 larger British Huntington's disease families. We suggest that although benign hereditary chorea and Huntington's disease may have some clinical similarities they are probably at two different loci.
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Affiliation(s)
- O W Quarrell
- Institute of Medical Genetics, University of Wales College of Medicine, Health Park, Cardiff
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29
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Maestri NE, Beaty TH, Folstein SE, Meyers DA. Use of the G8 probe in predicting risk of Huntington disease. AMERICAN JOURNAL OF MEDICAL GENETICS 1987; 28:989-97. [PMID: 2961260 DOI: 10.1002/ajmg.1320280426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Discovery of the linkage between the G8 probe and the gene for Huntington disease (HD) in families of varying ethnic origin, age-of-onset characteristics, and neurological symptomatology, makes it possible to use the G8 marker for presymptomatic testing of at-risk individuals. Risk estimates for such situations were calculated, using the program LIPED, with different G8 haplotype frequencies, different age-of-onset distributions, and varying amounts of family information. In the presence of untyped relatives, the resulting risk estimates can be extremely sensitive to G8 haplotype frequencies, and the higher risk was seen in individuals carrying rare haplotypes. Including haplotype information on distant relatives can also lead to greater variation in risk estimates. Changing the age-of-onset distribution had only a minimal effect on estimated risks; the largest effect was seen when informative at-risk sibs of the consultand were in their forties.
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Affiliation(s)
- N E Maestri
- Department of Epidemiology, School of Hygiene and Public Health, Johns Hopkins University, Baltimore, Maryland 21205
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30
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Abstract
Application of molecular biology, by means of linkage analysis and DNA probes that demonstrate restriction fragment length polymorphisms (RFLPs), has resulted in the chromosomal localization of the genes responsible for a number of neurological disorders. Characterization of the structure and function of individual genes for these diseases is in an early stage, but information available indicates that the molecular mechanisms underlying phenotypic expression of neurological diseases encompass a wide range of genetic errors ranging from the most minor (a single-base pair mutation) to large chromosomal deletions. Linkage analysis can now be used for genetic counseling in several of these disorders.
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Affiliation(s)
- J B Martin
- Neurology Service, Massachusetts General Hospital, Boston
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Gilliam TC, Tanzi RE, Haines JL, Bonner TI, Faryniarz AG, Hobbs WJ, MacDonald ME, Cheng SV, Folstein SE, Conneally PM. Localization of the Huntington's disease gene to a small segment of chromosome 4 flanked by D4S10 and the telomere. Cell 1987; 50:565-71. [PMID: 2886227 DOI: 10.1016/0092-8674(87)90029-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder of late onset, characterized by progressive motor disturbance, psychological manifestations, and intellectual deterioration. The HD gene has been genetically mapped by linkage to the DNA marker D4S10, but the exact physical location of the HD defect has remained uncertain. To delineate critical recombination events revealing the physical position of the HD gene, we have identified restriction fragment length polymorphisms for two recently mapped chromosome 4 loci, RAF2 and D4S62, and determined the pattern of segregation of these markers in both reference and HD pedigrees. Multipoint linkage analysis of the new markers with D4S10 and HD establishes that the HD gene is located in a very small physical region at the tip of the chromosome, bordered by D4S10 and the telomere. A crossover within the D4S10 locus orients this segment on the chromosome, providing the necessary information for efficient application of directional cloning strategies for progressing toward, and eventually isolating, the HD gene.
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32
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Robinson A. Genetics and the future of medicine. SOMATIC CELL AND MOLECULAR GENETICS 1987; 13:485-9. [PMID: 3331835 DOI: 10.1007/bf01534953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- A Robinson
- National Jewish Center for Immunology and Respiratory Medicine, Denver, Colorado
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33
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Abstract
DNA-based carrier testing and prenatal diagnosis are rapidly expanding medical applications of recombinant-DNA technology. The ultimate goal of DNA-based diagnosis is the determination of the causative mutation, but, in general, this is possible only for large deletions, insertions, or certain nonsense mutation that, in most diseases, involve only a few percent of affected families. If direct diagnosis of the carrier state or fetal disease state is not feasible, indirect diagnosis can be performed by following the segregation of linked polymorphisms through the family pedigree. For such indirect diagnosis, DNA from multiple family members must be analyzed. Although this procedure is highly accurate in many families, errors can potentially occur because of meiotic recombination, genetic heterogeneity, new mutations, and nonpaternity. In this review, a general introduction to DNA-based diagnosis of mendelian diseases is presented and the methods and strategy are outlined. The use of these techniques for the diagnosis of hemophilia A is then described to illustrate the principles of diagnosis and to highlight some of the complexities encountered. DNA-based diagnosis is in its infancy and has the potential to revolutionize preventive medicine.
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Mastromauro C, Myers RH, Berkman B. Attitudes toward presymptomatic testing in Huntington disease. AMERICAN JOURNAL OF MEDICAL GENETICS 1987; 26:271-82. [PMID: 2949611 DOI: 10.1002/ajmg.1320260205] [Citation(s) in RCA: 116] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
One hundred thirty-one individuals at 50% risk of inheriting Huntington disease (HD) responded to a survey to study their attitudes toward taking a genetic test based on the identification of a genetically linked DNA polymorphism. Ninety-six percent of the respondents believe that presymptomatic testing should be available, and 66% say they will use it themselves. Fewer married individuals, in comparison to those single, separated, and divorced, intend to take the test. Many respondents (40%) said their primary reason for wanting to be tested is to end the uncertainty in their lives. Results suggest that there will be self-selection in test use, with many individuals who believe they will be depressed or possibly suicidal with a positive test result deciding not to be tested or unsure about testing. However, 15% of those who want to be tested acknowledge that they may be at risk for suicide if they are probable gene carriers. Only 12% of all respondents say they will be likely to use prenatal testing, suggesting that initial demand may be low in New England. Implementation of presymptomatic testing challenges health care providers to develop strategies to care for otherwise healthy persons who will be given a diagnosis years before the onset of illness.
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Smurl JF, Weaver DD. Presymptomatic testing for Huntington chorea: guidelines for moral and social accountability. AMERICAN JOURNAL OF MEDICAL GENETICS 1987; 26:247-57. [PMID: 2949609 DOI: 10.1002/ajmg.1320260203] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Clinical trials of a presymptomatic test for Huntington chorea (HC) are beginning, and the test may set precedents in screening for other genetic disorders in this way. Therefore, it seems an opportune time to consider the moral and social implications of such testing. The strategy proposed here takes the form of guidelines for research, development, and clinical application of the HC test and any future similar tests. The guidelines cover four stages (preliminary research, verification, refinement, and clinical application). They draw on past experience, on existing guidelines for research involving human subjects, and on some general moral and legal principles. In addition to traditional concerns about relationships between counselors and consultants, they emphasize more contemporary concerns about the interests of third parties and social institutions in what occurs in modern methods of genetic screening. In all cases, however, the guidelines are provisional and are offered here mainly for purposes of discussion and to encourage similar efforts at policymaking by those who become involved with these forms of testing.
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Meissen GJ, Berchek RL. Intended use of predictive testing by those at risk for Huntington disease. AMERICAN JOURNAL OF MEDICAL GENETICS 1987; 26:283-93. [PMID: 2949612 DOI: 10.1002/ajmg.1320260206] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Huntington disease (HD) is a late-onset genetic disorder that is incurable and undetectable until the onset of symptoms. A marker for the gene that causes HD was recently discovered that will lead to a predictive test. The purpose of this research was to assess the attitudes, beliefs, and behavioral intentions concerning the impending predictive test by those at risk for HD. Results from a sample of 56 at-risk individuals indicated that a majority (65%) favored using the presymptomatic test and would encourage their adult children to use it as well. Fewer but still a substantial percentage of respondents would use the prenatal test (42%) and would test at-risk minors (35%). Surprisingly, knowledge about predictive testing was quite low and a majority of those least knowledgeable about predictive testing intended to use the test. These findings emphasized the need for outreach and prevention efforts to prepare the at risk and specialized programs of genetic counseling and follow up to accompany predictive testing.
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Bird TD, Hewitt J, Conneally PM, Hayden MR. Linkage of the G8 marker on chromosome 4 to Huntington's disease in a large American black family. N Engl J Med 1986; 315:1165-6. [PMID: 2945112 DOI: 10.1056/nejm198610303151815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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40
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Youngman S, Sarfarazi M, Quarrell OW, Conneally PM, Gibbons K, Harper PS, Shaw DJ, Tanzi RE, Wallace MR, Gusella JF. Studies of a DNA marker (G8) genetically linked to Huntington disease in British families. Hum Genet 1986; 73:333-9. [PMID: 3017842 DOI: 10.1007/bf00279096] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Close genetic linkage has been shown between the DNA sequence G8 (locus D4S10) and 16 British families with Huntington disease using the HindIII, EcoR1, Nci1, and Pst1 polymorphisms detected by G8, and by combining all the polymorphisms to give a combined haplotype. Two recombinants have been detected in these families giving a maximum lod score of 17.60 at a theta of 0.02. These results confirm the originally reported linkage between the loci and provide evidence against significant multilocus heterogeneity for Huntington disease.
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41
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Craufurd DI, Harris R. Ethics of predictive testing for Huntington's chorea: the need for more information. BMJ : BRITISH MEDICAL JOURNAL 1986; 293:249-51. [PMID: 2942216 PMCID: PMC1341184 DOI: 10.1136/bmj.293.6541.249] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The finding of a genetically linked polymorphic DNA marker has made possible a predictive test for Huntington's chorea. This DNA probe has so far been used only for research and has technical limitations, but some workers now wish to apply it to clinical predictions. Those identified by the probe as being probable carriers of the Huntington's chorea gene would be exposed to uncertain psychological risks and social pressures. Ethical guidelines should be established, but these require greater knowledge of the potential benefits and hazards of this powerful new procedure. Controlled clinical trials are urgently needed.
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42
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Gusella JA, Gilliam TC, MacDonald ME, Cheng SV, Tanzi RE. Molecular genetics of human chromosome 4. J Med Genet 1986; 23:193-9. [PMID: 2941587 PMCID: PMC1049626 DOI: 10.1136/jmg.23.3.193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The recent discovery that the gene causing Huntington's disease (HD) resides on chromosome 4 has generated increased interest in this autosome. Chromosome 4 contains two of the more informative conventional genetic markers, GC and MNS, but most loci have been assigned to it by recombinant DNA techniques. There are currently more anonymous DNA fragments detecting restriction fragment length polymorphisms (RFLPs) on chromosome 4 than on any other autosome. In addition, most of the cloned genes from this chromosome detect useful RFLPs. A genetic linkage map including both conventional and DNA markers should soon span the entire chromosome and will undoubtedly lead to the localisation of other inherited disorders.
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Abstract
Recombinant DNA technology promises to make an important contribution to the analysis and diagnosis of inherited human disease. Direct detection and analysis of various genetic defects at the DNA level are now possible using cloned gene or oligonucleotide probes. In addition, the use of restriction fragment length polymorphisms associated with linked DNA segments should permit not only the diagnosis of hitherto undetectable disease states but also the chromosomal localization of the loci responsible. The eventual isolation of disease loci should lead to a better understanding of the molecular basis of inherited disease.
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Pericak-Vance MA, Meyers DA, Gusella JF, Folstein SE, Conneally PM. Genetic analysis workshop IV: Huntington disease linkage analysis, data description. Genet Epidemiol 1986. [DOI: 10.1002/gepi.1370030730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Pericak-Vance MA, Meyers DA. Genetic analysis workshop IV: Huntington disease linkage analysis summary. Genet Epidemiol 1986; 1:197-209. [PMID: 2952549 DOI: 10.1002/gepi.1370030731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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48
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49
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Badner JA, Chakravarti A, Buetow KH. Linkage analysis between Huntington disease and the G8 marker locus. Genet Epidemiol 1986; 1:211-6. [PMID: 2883077 DOI: 10.1002/gepi.1370030732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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50
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Sarfarazi M. Report on genetic linkage analysis between Huntington's disease and the G8 DNA polymorphism. Genet Epidemiol 1986; 1:259-64. [PMID: 2883084 DOI: 10.1002/gepi.1370030740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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