Genetic Analysis of Otosclerosis Families

Genomic DNA was isolated from peripheral leukocytes according to a standard salting out procedure (Miller et al. 1988 (link)). Microsatellite markers were fluorescently labeled and amplified by PCR, run on ABI 3130xl or 3730 (Applied Biosystems) and analyzed with Gene Mapper v4.0. Pedigrees were drawn with Progeny (Progeny Genetics LLC) and haplotypes phased manually with the least number of recombination events. To test for linkage in the NL family, five affected members (PIDs II-2, II-3, II-6, II-9, III-2; otosclerosis confirmed by surgery) and two of unknown clinical status (PIDs III-5, III-6) (Fig. 2a) were genotyped for markers spanning each OTSC disease interval and bracketing three otosclerosis susceptibility genes (Supplementary Table 1). As well, a total of 17 relatives were genotyped with nine extra markers (D16S518, D16S3049, D16S3098, D16S422, D16S2625, D16S520, D16S413, D16S3023, D16S3026) mapping qter of the OTSC4 disease interval. Two-point parametric linkage analyses (MLINK ver 5.1) were run for three markers per locus (assuming autosomal dominant inheritance, 99% penetrance and a gene frequency of 0.00). LOD scores were calculated at recombination fractions 0.000 to 0.5000. The proband was also sequenced for rare otosclerosis-associated variants in SERPINF1 (Ziff et al. 2016 (link)).

Free full text: Click here

Abdelfatah N., Mostafa A.A., French C.R., Doucette L.P., Penney C., Lucas M.B., Griffin A., Booth V., Rowley C., Besaw J.E., Tranebjærg L., Rendtorff N.D., Hodgkinson K.A., Little L.A., Agrawal S., Parnes L., Batten T., Moore S., Hu P., Pater J.A., Houston J., Galutira D., Benteau T., MacDonald C., French D., O’Rielly D.D., Stanton S.G, & Young T.L. (2021). A pathogenic deletion in Forkhead Box L1 (FOXL1) identifies the first otosclerosis (OTSC) gene. Human Genetics, 141(3-4), 965-979.

Publication 2021

ABI 3130xl Gene Mapper v4.0

Autosomal dominant Genes Genomic Haplotypes Inheritance Leukocytes Linkage analyses Microsatellite markers Otosclerosis Otsc4 Pids Recombination Sequenced variants Surgery Susceptibility

Corresponding Organization : Memorial University of Newfoundland

Other organizations : Western University, University of Toronto, Rigshospitalet, University of Copenhagen, London Health Sciences Centre, University of Manitoba, St. John’s Health Sciences Centre

Top 5 similar protocols

Variable analysis

independent variables

Microsatellite markers
Markers spanning each OTSC disease interval
Nine extra markers (D16S518, D16S3049, D16S3098, D16S422, D16S2625, D16S520, D16S413, D16S3023, D16S3026) mapping qter of the OTSC4 disease interval

dependent variables

Microsatellite marker amplification by PCR
Genotyping of affected and unknown clinical status members of the NL family
Two-point parametric linkage analyses
LOD scores at recombination fractions 0.000 to 0.5000
Sequencing of the proband for rare otosclerosis-associated variants in SERPINF1

control variables

Autosomal dominant inheritance
99% penetrance
Gene frequency of 0.00

positive controls

Five affected members (PIDs II-2, II-3, II-6, II-9, III-2) with otosclerosis confirmed by surgery

negative controls

Two members (PIDs III-5, III-6) of unknown clinical status

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!