Swedish population substructure revealed by genome-wide single nucleotide polymorphism data.

The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes--especially southern Swedes--were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of Norrland probably result mainly from isolation by distance and genetic drift caused by low population density. The internal structure within Sweden (F(ST) = 0.0005 between provinces) was stronger than that in many Central European populations, although smaller than what has been observed for instance in Finland; importantly, it is of the magnitude that may hamper association studies with a moderate number of markers if cases and controls are not properly matched geographically. Overall, our results underline the potential of genome-wide data in analyzing substructure in populations that might otherwise appear relatively homogeneous, such as the Swedes.

Genomic landscape of positive natural selection in Northern European populations.

Analyzing genetic variation of human populations for detecting loci that have been affected by positive natural selection is important for understanding adaptive history and phenotypic variation in humans. In this study, we analyzed recent positive selection in Northern Europe from genome-wide data sets of 250 000 and 500 000 single-nucleotide polymorphisms (SNPs) in a total of 999 individuals from Great Britain, Northern Germany, Eastern and Western Finland, and Sweden. Coalescent simulations were used for demonstrating that the integrated haplotype score (iHS) and long-range haplotype (LRH) statistics have sufficient power in genome-wide data sets of different sample sizes and SNP densities. Furthermore, the behavior of the F(ST) statistic in closely related populations was characterized by allele frequency simulations. In the analysis of the North European data set, 60 regions in the genome showed strong signs of recent positive selection. Out of these, 21 regions have not been discovered in previous scans, and many contain genes with interesting functions (eg, RAB38, INFG, NOS1AP, and APOE). In the putatively selected regions, we observed a statistically significant overrepresentation of genetic association with complex disease, which emphasizes the importance of the analysis of positive selection in understanding the evolution of human disease. Altogether, this study demonstrates the potential of genome-wide data sets to discover loci that lie behind evolutionary adaptation in different human populations.

Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe.

BACKGROUND: Genome-wide data provide a powerful tool for inferring patterns of genetic variation and structure of human populations. PRINCIPAL FINDINGS: In this study, we analysed almost 250,000 SNPs from a total of 945 samples from Eastern and Western Finland, Sweden, Northern Germany and Great Britain complemented with HapMap data. Small but statistically significant differences were observed between the European populations (F(ST) = 0.0040, p<10(-4)), also between Eastern and Western Finland (F(ST) = 0.0032, p<10(-3)). The latter indicated the existence of a relatively strong autosomal substructure within the country, similar to that observed earlier with smaller numbers of markers. The Germans and British were less differentiated than the Swedes, Western Finns and especially the Eastern Finns who also showed other signs of genetic drift. This is likely caused by the later founding of the northern populations, together with subsequent founder and bottleneck effects, and a smaller population size. Furthermore, our data suggest a small eastern contribution among the Finns, consistent with the historical and linguistic background of the population. SIGNIFICANCE: Our results warn against a priori assumptions of homogeneity among Finns and other seemingly isolated populations. Thus, in association studies in such populations, additional caution for population structure may be necessary. Our results illustrate that population history is often important for patterns of genetic variation, and that the analysis of hundreds of thousands of SNPs provides high resolution also for population genetics.

Clinical expression of Leber hereditary optic neuropathy is affected by the mitochondrial DNA-haplogroup background.

Leber hereditary optic neuropathy (LHON) is due primarily to one of three common point mutations of mitochondrial DNA (mtDNA), but the incomplete penetrance implicates additional genetic or environmental factors in the pathophysiology of the disorder. Both the 11778G-->A and 14484T-->C LHON mutations are preferentially found on a specific mtDNA genetic background, but 3460G-->A is not. However, there is no clear evidence that any background influences clinical penetrance in any of these mutations. By studying 3,613 subjects from 159 LHON-affected pedigrees, we show that the risk of visual failure is greater when the 11778G-->A or 14484T-->C mutations are present in specific subgroups of haplogroup J (J2 for 11778G-->A and J1 for 14484T-->C) and when the 3460G-->A mutation is present in haplogroup K. By contrast, the risk of visual failure is significantly less when 11778G-->A occurs in haplogroup H. Substitutions on MTCYB provide an explanation for these findings, which demonstrate that common genetic variants have a marked effect on the expression of an ostensibly monogenic mtDNA disorder.

Epidemiology and penetrance of Leber hereditary optic neuropathy in Finland.

We have performed an entire-population-based survey of the epidemiology and penetrance of Leber hereditary optic neuropathy (LHON) in Finland - a country that is among the best-studied genetic isolates in the world. During our long-term clinical follow-up period since 1970, we have so far identified 36 LHON families in Finland, comprised of almost 1000 family members. Counting the unaffected family members has been possible thanks to accessible genealogical records, and this has improved the accuracy of our penetrance figures by minimizing the sample bias. Our results, although confirming some well-known features of LHON, indicate that the overall penetrance of LHON is lower than previously estimated, and that affected females have a higher incidence of affected offspring compared to the unaffected females. The prevalence of LHON in Finland is 1:50 000, and one in 9000 Finns is a carrier of one of the three LHON primary mutations.

Delineation of the ADULT syndrome phenotype due to arginine 298 mutations of the p63 gene.

The ADULT syndrome (Acro-Dermato-Ungual-Lacrimal-Tooth, OMIM 103285) is a rare ectodermal dysplasia associated with limb malformations and caused by heterozygous mutations in p63. ADULT syndrome has clinical overlap with other p63 mutation syndromes, such as EEC (OMIM 604292), LMS (OMIM 603543), AEC (106260), RHS (129400) and SHFM4 (605289). ADULT syndrome characteristics are ectrodactyly, ectodermal dysplasia, mammary gland hypoplasia and normal lip and palate. The latter findings allow differentiation from EEC syndrome. LMS differs by milder ectodermal involvement. Here, we report three new unrelated ADULT syndrome families, all with mutations of arginine 298. On basis of 16 patients in five families with R298 mutation, we delineate the ADULT syndrome phenotype. In addition, we have documented a gain-of-function effect on the dNp63gamma isoform caused by this mutation. We discuss the possible relevance of oral squamous cell carcinoma in one patient, who carries this p63 germline mutation.

Regional differences among the Finns: a Y-chromosomal perspective.

Twenty-two Y-chromosomal markers, consisting of fourteen biallelic markers (YAP/DYS287, M170, M253, P37, M223, 12f2, M9, P43, Tat, 92R7, P36, SRY-1532, M17, P25) and eight STRs (DYS19, DYS385a/b, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393), were analyzed in 536 unrelated Finnish males from eastern and western subpopulations of Finland. The aim of the study was to analyze regional differences in genetic variation within the country, and to analyze the population history of the Finns. Our results gave further support to the existence of a sharp genetic border between eastern and western Finns so far observed exclusively in Y-chromosomal variation. Both biallelic haplogroup and STR haplotype networks showed bifurcated structures, and similar clustering was evident in haplogroup and haplotype frequencies and genetic distances. These results suggest that the western and eastern parts of the country have been subject to partly different population histories, which is also supported by earlier archaeological, historical and genetic data. It seems probable that early migrations from Finno-Ugric sources affected the whole country, whereas subsequent migrations from Scandinavia had an impact mainly on the western parts of the country. The contacts between Finland and neighboring Finno-Ugric, Scandinavian and Baltic regions are evident. However, there is no support for recent migrations from Siberia and Central Europe. Our results emphasize the importance of incorporating Y-chromosomal data to reveal the population substructure which is often left undetected in mitochondrial DNA variation. Early assumptions of the homogeneity of the isolated Finnish population have now proven to be false, which may also have implications for future association studies.

Identification of an X-chromosomal locus and haplotype modulating the phenotype of a mitochondrial DNA disorder.

Mitochondrial DNA (mtDNA) mutations are a major cause of human disease. A large number of different molecular defects ultimately compromise oxidative phosphorylation, but it is not clear why the same biochemical defect can cause diverse clinical phenotypes. There is emerging evidence that nuclear genes modulate the phenotype of primary mtDNA disorders. Here, we define an X-chromosomal haplotype that interacts with specific MTND mutations to cause visual failure in the most common mtDNA disease, Leber hereditary optic neuropathy. This effect is independent of the mtDNA genetic background and explains the variable penetrance and sex bias that characterizes this disorder.

Dominant optic atrophy: correlation between clinical and molecular genetic studies.

PURPOSE: To assess the clinical picture and molecular genetics of 14 Finnish families with dominant optic atrophy (DOA). METHODS: The clinical status of family members was based on the assessment of visual acuity, colour vision, visual fields and optic nerve appearance; 31 individuals were affected, two suspect and 21 unaffected. A total of 30 coding exons and exon- intron boundaries of the OPA1 gene were sequenced in order to detect mutations. RESULTS: Half the patients were diagnosed at the age of < or = 20 years. Ten out of 20 affected individuals followed up for > or = 6 years had a progressive disease and 10 had a stable disease. According to WHO criteria, 36% of the affected patients were visually handicapped. Eight OPA1 pathogenic mutations, all but one novel, and 18 neutral polymorphisms were detected. CONCLUSION: The most sensitive indicators of DOA were optic disc pallor and dyschromatopsia. With molecular genetic analysis, asymptomatic mutation carriers and DOA cases with a mild clinical outcome were ascertained. No mutational hotspot or Finnish major mutation in the OPA1 gene could be demonstrated as most families carried a unique mutation. No obvious genotype- phenotype correlation could be detected. Detailed clinical assessment and exclusion of non-DOA families prior to mutation screening are necessary for obtaining a high mutation detection rate.

Isolation of transcriptomal changes attributable to LHON mutations and the cybridization process.

Leber's hereditary optic neuropathy (LHON) is thought to be the most common disease resulting from mitochondrial DNA (mtDNA) point mutations, and transmitochondrial cytoplasmic hybrid (cybrid) cell lines are the most frequently used model for understanding the pathogenesis of mitochondrial disorders. We have used oligonucleotide microarrays and a novel study design based on shared transcripts to allocate transcriptomal changes into rho-zero-dependent, cybridization-dependent and LHON-dependent categories in these cells. The analysis indicates that the rho-zero process has the largest transcriptomal impact, followed by the cybridization process, and finally the LHON mutations. The transcriptomal impacts of the rho-zero and cybridization processes preferentially and significantly affect the mitochondrial compartment, causing upregulation of many transcripts involved in oxidative phosphorylation, presumably in response to the mtDNA depletion that occurs at the rho-zero step. Nine LHON-specific transcriptional alterations were shared among osteosarcoma cybrids and lymphoblasts bearing LHON mutations. Notably, the aldose reductase transcript was overexpressed in LHON cybrids and lymphoblasts. Aldose reductase is also overexpressed in diabetic retinopathy, leading to optic nerve and retinal complications. The LHON-specific increase in transcript level was confirmed by quantitative reverse transcription-polymerase chain reaction (RT-PCR), and a western blot confirmed a higher level of aldose reductase in mutant mitochondria. One product of aldose reductase is sorbitol, which has been linked to osmotic stress, oxidative stress and optic neuropathy, and sorbitol levels were increased in LHON cybrids. If these results are confirmed in patient tissues, aldose reductase inhibitors could have some therapeutic value for LHON.

Detection of the founder effect in Finnish CADASIL families.

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited cerebrovascular disease characterized by brain infarcts, cognitive decline and dementia. The disease is caused by at least 91 missense mutations, four deletions and one splice site mutation in the NOTCH3 gene, which maps to 19p13.1. In 18 out of the 21 Finnish CADASIL families so far identified, the causative mutation is an arginine to cysteine substitution in position 133 (R133C). Most of the families carrying this mutation originate from the western coast of Finland, thus suggesting a founder effect. No previous reports of a founder effect in CADASIL have been published. We haplotyped 60 patients from these 18 families for 10 microsatellite markers in order to determine whether the families descend from a common ancestor. We found a similar haplotype linked to the mutation in all 18 pedigrees, which indicates a single common ancestor for all the Finnish R133C families. The age analysis of the founder mutation places the introduction of the mutation in the late 1600s or early 1700s.

Absence of the genetic variant Val79Met in human chorionic gonadotropin-beta gene 5 in five European populations.

Chorionic gonadotropin (CG) is an essential signal in establishment and maintenance of pregnancy in humans and higher primates. A G-to-A transition in exon 3 of human CGbeta gene 5, changing the naturally occurring valine residue to methionine in codon 79 (Val(79)Met) has been reported at carrier frequency 4.2% in a random population from the Midwest of the United States. The biological activity of the variant hCG was similar to that of wild-type (WT) hCG. However, the Val(79)Met beta-subunit displayed impaired ability to assemble with alpha-subunit, and the amount of hCG alpha/beta heterodimers formed and secreted by transfected cells was seriously impaired in the previous study. Because of these functional implications we found it important to study the occurrence of the Val(79)Met hCGbeta variant in other populations. By using a PCR-RFLP method, a search for the Val(79)Met hCGbeta variant was carried out on a total of 580 DNA samples from five European populations (Finland, Denmark, Greece, Germany and the UK). The results demonstrated an absence of the polymorphism in these populations. Hence, the naturally occurring variant (Val(79)Met) of the hCGbeta gene 5, found previously at high frequency in the US, is clearly less common, or absent, in the European populations studied.

A novel sequence variation in the transactivation regulating domain of the androgen receptor in two infertile Finnish men.

OBJECTIVE: To study a new sequence variant at the beginning of the CAG repeat in the exon 1 of the androgen receptor gene. DESIGN: Controlled clinical study. SETTINGS: Healthy volunteers in an academic research environment. PATIENT(S): Sixty-two Finnish men with spermatogenic failure and 60 controls. INTERVENTION(S): ABI PRISM 377 (Applied Biosystems, Foster City, CA) automated sequencing. MAIN OUTCOME MEASURE(S): Determining the sequence around the CAG repeat of the AR gene. RESULT(S): A new 173A-->T (Q58L) substitution at the beginning of the CAG repeat in the transactivation-regulating domain of the androgen receptor was found in 2 infertile Finnish men but not in 60 other infertile men or 60 controls. CONCLUSION(S): As the polyglutamine tract coded by the CAG repeat is crucial to spermatogenesis, the 173A-->T (Q58L) substitution might be the cause of infertility in these two Finnish men.

Long CAG repeats in the AR gene are not associated with infertility in Finnish males.

BACKGROUND: The modulatory domain of the human androgen receptor gene contains a polymorphic CAG repeat coding for a polyglutamine tract. The length of the polyglutamine tract is inversely correlated with transcriptional activity of the androgen receptor. As androgens are crucial to spermatogenesis, decreased transcriptional activity of the androgen receptor associated with a long polyglutamine tract could lead to failure in spermatogenesis. Accordingly, long CAG repeats within the normal range have been suggested to be more common in infertile males than in the control population. METHODS: To test this hypothesis, we examined the CAG repeat number of 192 Finnish males with moderate or severe spermatogenic failure and 149 control males. RESULTS: Our results did not support the hypothesis, the controls harbored slightly longer CAG repeats than the infertile males. CONCLUSION: At least in the present study population from Finland, long CAG repeats in the androgen receptor gene do not play a significant role in spermatogenic failure.

Promoter analysis of the human SLC7A7 gene encoding y+L amino acid transporter-1 (y+LAT-1).

The human SLC7A7 gene on chromosome 14q11.2 encodes the y+L amino acid transporter-1 (y+LAT-1) protein that transports, together with the 4F2hc cell surface antigen, cationic amino acids through the basolateral membrane of epithelial cells in the small intestine and kidney. The SLC7A7 gene comprises 11 exons, but the first two are not translated. Mutations in the coding region of the SLC7A7 gene cause a rare autosomal disorder, lysinuric protein intolerance (LPI). We have now investigated the expression levels and putative 5' promoter elements of the SLC7A7. The 5' region of the first untranslated exon contains no TATA-box, Inr elements nor other classical promoter elements, but has instead other putative transcription factor binding sequences. The E-box and AP-2 elements were able to bind proteins in HEK293 cells and adult kidney tissue extracts, but not in fibroblasts. Using transient transfection and luciferase reporter gene studies, we showed that the first two introns located in the untranslated region contained transcriptional enhancer elements. Northern blot analysis showed low and equal SLC7A7 mRNA levels in the control and LPI patient fibroblastoid and lymphoblast cells.

Segregation of the ND4/11778 and the ND1/3460 mutations in four heteroplasmic LHON families.

Leber hereditary optic neuropathy (LHON) is an ocular disease associated with mutations in the mitochondrial DNA (mtDNA). The level of heteroplasmy in the mtDNA mutations ND4/11778 and ND1/3460 was followed over a period of 4-12 years in blood samples taken from nine members of four heteroplasmic LHON families. In addition, hair follicle and urinary tract epithelium samples of one individual were studied. The quantification of heteroplasmy was performed using the solid-phase minisequencing method. Only minor and random shifts in the heteroplasmy levels were observed over time, but there were no systematic changes towards an increasing or decreasing proportion of either LHON mutant in the individuals. This indicates that there is no selection for either mtDNA genotype but the segregation of the wild-type mtDNAs and those carrying LHON mutations is a stochastic process governed by random genetic drift. In this respect, LHON mutations seem to behave like neutral polymorphisms.

Identification of an intronic TG repeat polymorphism in the human proteasome core particle PROS-27K gene.

A TG dinucleotide repeat was identified in intron 6 of the human proteasome core particle PROS-27K (IOTA, PSMA6) gene. We present data on the length polymorphism of this repeat in 120 individuals from Latvia and 197 individuals from Finland. A combination of PCR and fluorescent gel electrophoresis was utilized to type the polymorphism. Twelve alleles were observed, varying in length from 10 to 23 TG repeats. Similar allele frequencies were observed in Latvian and Finnish subjects, with 17 and 20 repeats being the most frequent in both populations. We suggest that this TG dinucleotide repeat could be utilized as a prospective marker for genetic linkage and association studies of common diseases.

Y-chromosomal diversity suggests that Baltic males share common Finno-Ugric-speaking forefathers.

OBJECTIVE: To elucidate the genetic relationships between Estonian, Latvian and Lithuanian men by studying Y-chromosomal variation in these people. METHODS: The allelic status of five deep-rooted marker loci (YAP, Tat, M9, 92R7 and SRY-1532) was determined for 346 Baltic males. On the basis of single nucleotide polymorphism (SNP) haplotypes, Y chromosomes were divided into six haplogroups, and the Baltic haplogroup distribution compared with that in 7 European reference populations. Haplogroup frequencies, diversities and genetic distances (F(ST) values) were calculated. The relationships between populations were further illustrated using Mantel test, neighbor-joining tree and principal-component map. RESULTS: We found the Indo-European-speaking Latvians and Lithuanians to be genetically very similar to the Finno-Ugric-speaking Estonians. When compared to the reference populations, Baltic males were most closely related to the Finno-Ugric-speaking Mari, followed by their Finnish and Slavonic neighbors. CONCLUSIONS: The genetic similarity existing between Estonian, Latvian and Lithuanian men suggests that they originate from the same male founder population. Since the Baltic Y-chromosomal haplogroup distribution more closely resembles that of Finno-Ugric than Indo-European-speaking populations, we propose a hypothesis that Baltic males share a common Finno-Ugric ancestry.

A rare mitochondrial DNA haplotype observed in Koreans.

The haplogroup affiliations of Korean mitochondrial DNAs (mtDNAs) were determined by restriction analysis. Out of the 101 mtDNAs analyzed, 91 (90%) belonged to Asian-specific haplogroups M, C, D, G, A, B, and F. Haplogroup E was not detected among the Korean mtDNAs. Three mtDNAs represented an unusual mtDNA haplotype characterized by simultaneous presence of E and G haplogroup-specific polymorphisms. To characterize this haplotype in more detail, we sequenced the hypervariable segment I (HVSI) from these mtDNAs as well as from those from selected individuals representing each haplogroup. Sequence data were further used to compare Korean mtDNAs with mtDNAs from other Asian populations. The observed rare haplotype was also found among Japanese, which suggests that it is one of the ancestral lineages originally peopling Japan.