Construction of human linkage maps: Likelihood calculations for multilocus linkage analysis

Gm, Lathrop; Jm, Lalouel; White, R. W. G.

doi:10.1002/gepi.1370030105

Cited by 190 publications

(89 citation statements)

References 8 publications

(6 reference statements)

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“…Pairwise linkage analysis was performed using the LINKAGE package, [34][35][36] and the heterogeneity analysis using the program HOMOG. 37 Sib-pair analysis was done using the SIBPAIR program.…”

Section: Discussionmentioning

confidence: 99%

Linkage analysis of putative schizophrenia gene candidate regions on chromosomes 3p, 5q, 6p, 8p, 20p and 22q in a population-based sampled Finnish family set

et al. 1998

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During the past decade numerous studies have been published describing chromosomal regions potentially linked with schizophrenia. Unfortunately, none of these studies has been able to conclusively identify any specific gene that predisposes to schizophrenia. Typically evidence for linkage is seen on large chromosomal regions, as expected, containing tens or even hundreds of genes. Furthermore, attempts to replicate the findings have rarely been successful leaving a confusion about the existence of predisposing genes for schizophrenia in a particular region of the genome. We have carried out linkage analysis in a set of 62 pedigrees rising from a genetically isolated population of Finland with markers on six chromosomal regions earlier suggested to harbor predisposing genes for schizophrenia, namely 3p, 1 5q, 2,3 6p, 4 8p, 1 20p, 5 and 22q. 6,7 We were not able to find significant evidence for linkage on any of these chromosomal regions. However, some support for linkage was found on all studied chromosomal regions, except 3p.We identified all Finnish patients with schizophrenia born between 1940 and 1969 (n = 29 124). 8 Patients who had received disability pension or free medication because of schizophrenia were identified from two registers of the Social Insurance Institution, and patients who had been hospitalized for schizophrenia were identified from the National Hospital Discharge Register. All three registers were computerized in 1968; ICD-8 diagnostic criteria and codes were used before 1987, since when psychiatric diagnoses have been coded according to ICD-9 applying DSM-III-R diagnostic criteria. We accepted all probands with a 295 diagnosis according to the ICD-8 and ICD-9 numbering scheme; this includes patients with schizophrenia, schizophreniform disorder, and schizoaffective disorder. Parents and siblings were identified from the National Population Register, and information on these relatives was linked to the health care registers to obtain data on their hospital treatments, pensions, and free medications.From these pedigrees, families with at least three affected family members were identified (n = 312), and those with at least one unaffected and three affected children were asked to participate in the study. If both parents were affected, the family was excluded. Diagnoses were confirmed as described in methods. Some families refused to participate and some were excluded because of uncertain diagnoses, and finally 62 families were used for molecular genetic studies out of 102 families who were asked to participate. Three different diagnostic classes were constructed as follows: class 1 contained 137 cases of DSM-IV schizophrenia, class 2 added 23 cases with schizoaffective disorder, and class 3 another 29 individuals with schizophrenia spectrum conditions (schizophreniform disorder, schizotypal personality disorder, schizoid personality disorder, delusional disorder, brief psychotic disorder, and psychotic disorder NOS). Patients with bipolar disorder or major depressive disorder were classifie...

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Section: Discussionmentioning

confidence: 99%

Linkage analysis of putative schizophrenia gene candidate regions on chromosomes 3p, 5q, 6p, 8p, 20p and 22q in a population-based sampled Finnish family set

et al. 1998

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“…12 Two-point linkage analyses under both homogeneity and heterogeneity model were carried out using the MLINK program of the LINKAGE package. 17,18 The marker allele frequencies were estimated using the DOWN-FREQ 2.1 program. 19 Tests for heterogeneity and calculations of proportion of linked families (a) were carried out using the HOMOG 3.35 program.…”

Section: Statistical Analysesmentioning

confidence: 99%

Association of LOXL1 gene with Finnish exfoliation syndrome patients

et al. 2009

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In this study, three single-nucleotide polymorphisms (SNPs) on the lysyl oxidase-like 1 (LOXL1) gene associated with exfoliation syndrome (XFS) and exfoliation glaucoma (XFG) were investigated in the Finnish population. A case-control study of 59 sporadic patients with XFS, 82 with XFG, 71 with primary open-angle glaucoma (POAG) and 26 individuals without these disorders from the southern Finnish population, and a family study of an extended family with 28 patients with XFS or XFG and 92 unaffected relatives from Kö kar islands, Southwestern Finnish archipelago, were conducted. Anonymous blood donors (n¼404) were studied as population-based controls. Three SNPs, rs1048661 (R141L), rs3825942 (G153D) and rs2165241, of the LOXL1 gene were genotyped by PCR sequencing. Association and linkage analyses were carried out. In both case-control and family materials, significant association for allele G of rs1048661 (P¼2.65Â10 À5 ; P¼0.0007), allele G of rs3825942 (P¼2.24Â10 À8 ; P¼0.49) and allele T of rs2165241 (P¼2.62Â10 À13 ; Po0.0001) was found in XFS/XFG. However, linkage was not observed for LOXL1 risk alleles. The corresponding three-locus haplotype GGT increased the risk of XFS/ XFG nearly 15-fold relative to low-risk haplotype GAC (odds ratio (OR): 14.9, P¼1.6Â10 À16 ). In conclusion, the earlier reported polymorphisms of the LOXL1 gene showed significant association also in the Finnish population.

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“…The MLINK program of the LINKAGE package 39,40 was used for the two-point analyses. Both dominant and recessive analyses were performed with nearly complete penetrance and low phenocopy rate (dominant model 0.001, 0.999, 0.999; recessive model 0.001, 0.001, 0.999).…”

Section: Statistical Analysesmentioning

confidence: 99%

Genome-wide scan for loci of Asperger syndrome

et al. 2004

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Asperger syndrome (AS), characterised by inadequate social interaction, lack of empathy and a dependence of routines and rituals, is classified as belonging to the autism spectrum disorders (DSM-IV and ICD-10). Although the prevalence of AS has been estimated to range from 0.3 up to 48.4 per 10 000, the phenotype still remains relatively unrecognised by clinicians. Several reports, including the original description by Hans Asperger (1944), have suggested that AS has a strong genetic component. Here, we have performed a genome-wide scan on Finnish families ascertained for AS with a strictly defined phenotype. In the initial scan, Z max 41.5 was observed on nine chromosomal regions, 1q21-22, 3p14-24, 3q25-27, 4p14, 4q32, 6p25, 6q16, 13q31-33 and 18p11. In the fine mapping stage, the highest two-point LOD scores were observed on chromosomes 1q21-22 (D1S484, Z max dom ¼3.58), 3p14-24 (D3S2432, Z max dom ¼2.50) and 13q31-33 (D13S793, Z max dom ¼1.59). The loci on 1q21-22 and 3p14-24 overlap with previously published autism susceptibility loci, and the loci on 1q21-22 and 13q31-33 overlap with the reported schizophrenia susceptibility loci. The present study is the first genome-wide screen in AS and therefore replication data sets are needed to evaluate further the significance of the AS-loci identified here.

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Construction of human linkage maps: Likelihood calculations for multilocus linkage analysis

Cited by 190 publications

References 8 publications

Linkage analysis of putative schizophrenia gene candidate regions on chromosomes 3p, 5q, 6p, 8p, 20p and 22q in a population-based sampled Finnish family set

Linkage analysis of putative schizophrenia gene candidate regions on chromosomes 3p, 5q, 6p, 8p, 20p and 22q in a population-based sampled Finnish family set

Association of LOXL1 gene with Finnish exfoliation syndrome patients

Genome-wide scan for loci of Asperger syndrome

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