scholarly journals Unifying Ideas for Non-Parametric Linkage Analysis

2011 ◽  
Vol 71 (4) ◽  
pp. 267-280 ◽  
Author(s):  
Aaron G. Day-Williams ◽  
John Blangero ◽  
Thomas D. Dyer ◽  
Kenneth Lange ◽  
Eric M. Sobel
Keyword(s):  
Linkage Analysis ◽  
Parametric Linkage Analysis ◽  
Non Parametric

Multipoint and single point non-parametric linkage analysis with imperfect data

2003 ◽  
Vol 121B (1) ◽  
pp. 89-94 ◽  
Author(s):  
Patrick F. Sullivan ◽  
Benjamin M. Neale ◽  
Michael C. Neale ◽  
Edwin van den Oord ◽  
Kenneth S. Kendler
Keyword(s):  
Linkage Analysis ◽  
Single Point ◽  
Parametric Linkage Analysis ◽  
Imperfect Data ◽  
Non Parametric

scholarly journals Power of non-parametric linkage analysis in mapping genes contributing to human longevity in long-lived sib-pairs

2004 ◽  
Vol 26 (3) ◽  
pp. 245-253 ◽  
Author(s):  
Qihua Tan ◽  
J. H. Zhao ◽  
I. Iachine ◽  
J. Hjelmborg ◽  
W. Vach ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Human Longevity ◽  
Parametric Linkage Analysis ◽  
Sib Pairs ◽  
Non Parametric

No evidence of linkage between 7q33–36 locus (OTSC2) and otosclerosis in seven British Caucasian pedigrees

2007 ◽  
Vol 121 (12) ◽  
pp. 1140-1147 ◽  
Author(s):  
F Q Alzoubi ◽  
W R Ollier ◽  
R T Ramsden ◽  
S R Saeed
Keyword(s):  
Environmental Factors ◽  
Linkage Analysis ◽  
Genetic Linkage ◽  
Deoxyribonucleic Acid ◽  
Chromosome Region ◽  
Parametric Linkage Analysis ◽  
Linkage Score ◽  
Multipoint Linkage ◽  
Chromosome Regions ◽  
Non Parametric

AbstractBackground:The aetiology of otosclerosis is complex, and probably involves an interaction between genes and environmental factors. Previous studies have revealed genetic linkage with a number of chromosome regions, including position 7q33–36.Aim:To confirm whether linkage exists between otosclerosis and chromosome region 7q33–36.Materials and methods:Seven multiply affected families were ascertained. Deoxyribonucleic acid from members of these families was extracted, and six markers were genotyped to cover a 16 cM region at 7q33–36. Both parametric and non-parametric multipoint linkage analyses were performed.Results:Parametric multipoint linkage analysis excluded any linkage at 7q33–36 (logarithm of odds score <−4.0). Non-parametric linkage analysis also failed to confirm any linkage (non-parametric linkage < 1.66). When tested individually, pedigree four was the only one to show a significant non-parametric linkage score between D7s684 and D7s2513 (non-parametric linkage = 1.96).Conclusion:No linkage was detected between otosclerosis and the 7q33–36 region. This could be explained by the study's lack of power, due to the limited number of families available.

scholarly journals Obelisc: an identical-by-descent mapping tool based on SNP streak

2020 ◽  
Author(s):  
Kyuto Sonehara ◽  
Yukinori Okada
Keyword(s):  
Linkage Analysis ◽  
Supplementary Information ◽  
Model Parameters ◽  
Analysis Tool ◽  
Genetic Linkage Analysis ◽  
Recessive Inheritance ◽  
Parametric Linkage Analysis ◽  
Identical By Descent ◽  
Analytical Results ◽  
Non Parametric

Abstract Motivation Genetic linkage analysis has made a huge contribution to the genetic mapping of Mendelian diseases. However, most previously available linkage analysis methods have limited applicability. Since parametric linkage analysis requires predefined model of inheritance with a fixed set of parameters, it is inapplicable without fully structured pedigree information. Furthermore, the analytical results are dependent on the specification of model parameters. While non-parametric linkage analysis can avoid these problems, the runs of homozygosity (ROH) mapping, a widely used non-parametric linkage analysis method, can only deal with recessive inheritance. The implementation of non-parametric linkage analyses capable of dealing with both dominant and recessive inheritance has been required. Results We have developed the Obelisc (Observational linkage scan), a flexibly applicable user-friendly non-parametric linkage analysis tool, which also provides an intuitive visualization of the analytical results. Obelisc is based on the SNP streak approach, which does not require any predefined inheritance model with parameters. In contrast to the ROH mapping, the SNP streak approach is applicable to both dominant and recessive traits. To illustrate the performance of Obelisc, we generated a pseudo-pedigree from the publicly available BioBank Japan Project genome-wide genotype dataset (n &gt; 180 000). By applying Obelisc to this pseudo-pedigree, we successfully identified the regions with inherited identical-by-descent haplotypes shared among the members of the pseudo-pedigree, which was validated by the population-based haplotype phasing approach. Availability and implementation Obelisc is feely available at https://github.com/qsonehara/Obelisc as a python package with example datasets. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Pedigree-Based Gene Mapping Supports Previous Loci and Reveals Novel Suggestive Loci in Specific Language Impairment

2020 ◽  
Vol 63 (12) ◽  
pp. 4046-4061
Author(s):  
Erin M. Andres ◽  
Kathleen Kelsey Earnest ◽  
Shelley D. Smith ◽  
Mabel L. Rice ◽  
Muhammad Hashim Raza
Keyword(s):  
Linkage Analysis ◽  
Language Impairment ◽  
Specific Language Impairment ◽  
Suggestive Linkage ◽  
Lod Score ◽  
Specific Language ◽  
Parametric Linkage Analysis ◽  
Genome Wide ◽  
Age Appropriate ◽  
Language Measure

Purpose Specific language impairment (SLI) is characterized by a delay in language acquisition despite a lack of other developmental delays or hearing loss. Genetics of SLI is poorly understood. The purpose of this study is to identify SLI genetic loci through family-based linkage mapping. Method We performed genome-wide parametric linkage analysis in six families segregating with SLI. An age-appropriate standardized omnibus language measure was used to categorically define the SLI phenotype. Results A suggestive linkage region replicated a previous region of interest with the highest logarithm of odds (LOD) score of 2.40 at 14q11.2-q13.3 in Family 489. A paternal parent-of-origin effect associated with SLI and language phenotypes on a nonsynonymous single nucleotide polymorphism (SNP) in NOP9 (14q12) was reported previously. Linkage analysis identified a new SLI locus at 15q24.3-25.3 with the highest parametric LOD score of 3.06 in Family 315 under a recessive mode of inheritance. Suggestive evidence of linkage was also revealed at 4q31.23-q35.2 in Family 300, with the highest LOD score of 2.41. Genetic linkage was not identified in the other three families included in parametric linkage analysis. Conclusions These results are the first to report genome-wide suggestive linkage with a total language standard score on an age-appropriate omnibus language measure across a wide age range. Our findings confirm previous reports of a language-associated locus on chromosome 14q, report new SLI loci, and validate the pedigree-based parametric linkage analysis approach to mapping genes for SLI. Supplemental Material https://doi.org/10.23641/asha.13203218

Recent Advances in Gene Mapping of Skin Diseases: Pseudoxanthoma Elasticum: A Satisfying Sibling Study

1999 ◽  
Vol 3 (3) ◽  
pp. 154-156 ◽  
Author(s):  
Sherri J. Bale
Keyword(s):  
Linkage Analysis ◽  
Autosomal Recessive ◽  
Recent Progress ◽  
Autosomal Dominant ◽  
Skin Diseases ◽  
Pseudoxanthoma Elasticum ◽  
Molecular Defect ◽  
Parametric Linkage Analysis ◽  
Affected Sib Pair ◽  
Made In

Background: A review of the recent progress made in mapping of the hereditary skin disease pseudoxanthoma elasticum is presented. Methods: Affected sib pair methods, parametric linkage analysis, and linkage heterogeneity tests are reviewed as applied to the effort to identify the location of the pseudoxanthoma elasticum gene. Results: Families segregating either autosomal dominant or autosomal recessive pseudoxanthoma elasticum mapped to chromosome 16p13.1. Conclusion: There is a gene for pseudoxanthoma elasticum on chromosome 16p. The underlying molecular defect remains to be elucidated.

scholarly journals Parametric Linkage Analysis Identifies Five Novel Genome-Wide Significant Loci for Familial Lung Cancer

2016 ◽  
Vol 82 (1-2) ◽  
pp. 64-74 ◽  
Author(s):  
Anthony M. Musolf ◽  
Claire L. Simpson ◽  
Mariza de Andrade ◽  
Diptasri Mandal ◽  
Colette Gaba ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Linkage Analysis ◽  
Parametric Linkage Analysis ◽  
Genome Wide

scholarly journals False-positive rates in two-point parametric linkage analysis

2014 ◽  
Vol 8 (Suppl 1) ◽  
pp. S110 ◽  
Author(s):  
Silke Szymczak ◽  
Claire L Simpson ◽  
Cheryl D Cropp ◽  
Joan E Bailey-Wilson
Keyword(s):  
Linkage Analysis ◽  
False Positive ◽  
Parametric Linkage Analysis
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