Literature DB >> 15836805

AUTOGSCAN: powerful tools for automated genome-wide linkage and linkage disequilibrium analysis.

Tero Hiekkalinna1, Joseph D Terwilliger, Sampo Sammalisto, Leena Peltonen, Markus Perola.   

Abstract

Genome-wide linkage analysis using multiple traits and statistical software packages is a tedious process which requires a significant amount of manual file manipulation. Different linkage analysis programs require different input file formats, making the task of analyzing data with multiple methods even more time-consuming. We have developed a software tool, AUTOGSCAN, that automates file formatting, the running of statistical analyses, and the summarizing of resulting statistics for whole genome scans with a push of a button, using several independent, and often idiosyncratic, statistical software packages such as MERLIN, SOLAR and GENEHUNTER. We also describe a program, ANALYZE, designed to run qualitative linkage analysis with several different statistical strategies and programs to efficiently screen for linkage and linkage disequilibrium for a given discrete trait. The ANALYZE program can also be used by AUTOGSCAN in a genome-wide sense.

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Year:  2005        PMID： 15836805     DOI： 10.1375/1832427053435382

Source DB:  PubMed          Journal:  Twin Res Hum Genet        ISSN： 1832-4274            Impact factor:   1.587


  13 in total

1.  Linkage analysis of alternative anxiety phenotypes in multiply affected panic disorder families.

Authors:  Abby J Fyer; Ramiro Costa; Fatemeh Haghighi; Mark W Logue; James A Knowles; Myrna M Weissman; Susan E Hodge; Steven P Hamilton
Journal:  Psychiatr Genet       Date:  2012-06       Impact factor: 2.458

2.  A male-specific quantitative trait locus on 1p21 controlling human stature.

Authors:  S Sammalisto; T Hiekkalinna; E Suviolahti; K Sood; A Metzidis; P Pajukanta; H E Lilja; A Soro-Paavonen; M-R Taskinen; T Tuomi; P Almgren; M Orho-Melander; L Groop; L Peltonen; M Perola
Journal:  J Med Genet       Date:  2005-04-12       Impact factor: 6.318

3.  Independent replication and initial fine mapping of 3p21-24 in Asperger syndrome.

Authors:  K Rehnström; T Ylisaukko-oja; T Nieminen-von Wendt; S Sarenius; T Källman; E Kempas; L von Wendt; L Peltonen; I Järvelä
Journal:  J Med Genet       Date:  2006-02       Impact factor: 6.318

4.  A visual migraine aura locus maps to 9q21-q22.

Authors:  P Tikka-Kleemola; V Artto; S Vepsäläinen; E M Sobel; S Räty; M A Kaunisto; V Anttila; E Hämäläinen; M-L Sumelahti; M Ilmavirta; M Färkkilä; M Kallela; A Palotie; M Wessman
Journal:  Neurology       Date:  2010-04-13       Impact factor: 9.910

5.  Shared loci for migraine and epilepsy on chromosomes 14q12-q23 and 12q24.2-q24.3.

Authors:  A Polvi; A Siren; M Kallela; H Rantala; V Artto; E M Sobel; A Palotie; A-E Lehesjoki; M Wessman
Journal:  Neurology       Date:  2012-01-04       Impact factor: 9.910

6.  Genome-wide linkage screen for stature and body mass index in 3.032 families: evidence for sex- and population-specific genetic effects.

Authors:  Sampo Sammalisto; Tero Hiekkalinna; Karen Schwander; Sharon Kardia; Alan B Weder; Beatriz L Rodriguez; Alessandro Doria; Jennifer A Kelly; Gail R Bruner; John B Harley; Susan Redline; Emma K Larkin; Sanjay R Patel; Amy J H Ewan; James L Weber; Markus Perola; Leena Peltonen
Journal:  Eur J Hum Genet       Date:  2008-09-10       Impact factor: 4.246

7.  Study of a Swiss dopa-responsive dystonia family with a deletion in GCH1: redefining DYT14 as DYT5.

Authors:  C Wider; S Melquist; M Hauf; A Solida; S A Cobb; J M Kachergus; J Gass; K D Coon; M Baker; A Cannon; D A Stephan; D F Schorderet; J Ghika; P R Burkhard; G Kapatos; M Hutton; M J Farrer; Z K Wszolek; F J G Vingerhoets
Journal:  Neurology       Date:  2007-09-05       Impact factor: 9.910

8.  Multicenter dizygotic twin cohort study confirms two linkage susceptibility loci for body mass index at 3q29 and 7q36 and identifies three further potential novel loci.

Authors:  J Kettunen; M Perola; N G Martin; B K Cornes; S G Wilson; G W Montgomery; B Benyamin; J R Harris; D Boomsma; G Willemsen; J-J Hottenga; P E Slagboom; K Christensen; K O Kyvik; T I A Sørensen; N L Pedersen; P K E Magnusson; T Andrew; T D Spector; E Widen; K Silventoinen; J Kaprio; A Palotie; L Peltonen
Journal:  Int J Obes (Lond)       Date:  2009-09-01       Impact factor: 5.095

9.  Novel susceptibility locus at 22q11 for diabetic nephropathy in type 1 diabetes.

Authors:  Maija Wessman; Carol Forsblom; Mari A Kaunisto; Jenny Söderlund; Jorma Ilonen; Riitta Sallinen; Tero Hiekkalinna; Maija Parkkonen; Alexander P Maxwell; Lise Tarnow; Hans-Henrik Parving; Samy Hadjadj; Michel Marre; Leena Peltonen; Per-Henrik Groop
Journal:  PLoS One       Date:  2011-09-01       Impact factor: 3.240

10.  A potential novel spontaneous preterm birth gene, AR, identified by linkage and association analysis of X chromosomal markers.

Authors:  Minna K Karjalainen; Johanna M Huusko; Johanna Ulvila; Jenni Sotkasiira; Aino Luukkonen; Kari Teramo; Jevon Plunkett; Verneri Anttila; Aarno Palotie; Ritva Haataja; Louis J Muglia; Mikko Hallman
Journal:  PLoS One       Date:  2012-12-05       Impact factor: 3.240
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