Identification of C12orf4 as a gene for autosomal recessive intellectual disability.

Intellectual disability (ID) is a major health problem in our society. Genetic causes of ID remain unknown because of its vast heterogeneity. Here we report two Finnish families and one Dutch family with affected individuals presenting with mild to moderate ID, neuropsychiatric symptoms and delayed speech development. By utilizing whole exome sequencing (WES), we identified a founder missense variant c.983T>C (p.Leu328Pro) in seven affected individuals from two Finnish consanguineous families and a deletion c.799_1034-429delinsTTATGA (p.Gln267fs) in one affected individual from a consanguineous Dutch family in the C12orf4 gene on chromosome 12. Both the variants co-segregated in the respective families as an autosomal recessive trait. Screening of the p.Leu328Pro variant showed enrichment in the North Eastern sub-isolate of Finland among anonymous local blood donors with a carrier frequency of 1:53, similar to other disease mutations with a founder effect in that region. To date, only one Arab family with a three affected individuals with a frameshift insertion variant in C12orf4 has been reported. In summary, we expand and establish the clinical and mutational spectrum of C12orf4 variants. Our findings implicate C12orf4 as a causative gene for autosomal recessive ID.

A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions.

Humans have developed the perception, production and processing of sounds into the art of music. A genetic contribution to these skills of musical aptitude has long been suggested. We performed a genome-wide scan in 76 pedigrees (767 individuals) characterized for the ability to discriminate pitch (SP), duration (ST) and sound patterns (KMT), which are primary capacities for music perception. Using the Bayesian linkage and association approach implemented in program package KELVIN, especially designed for complex pedigrees, several single nucleotide polymorphisms (SNPs) near genes affecting the functions of the auditory pathway and neurocognitive processes were identified. The strongest association was found at 3q21.3 (rs9854612) with combined SP, ST and KMT test scores (COMB). This region is located a few dozen kilobases upstream of the GATA binding protein 2 (GATA2) gene. GATA2 regulates the development of cochlear hair cells and the inferior colliculus (IC), which are important in tonotopic mapping. The highest probability of linkage was obtained for phenotype SP at 4p14, located next to the region harboring the protocadherin 7 gene, PCDH7. Two SNPs rs13146789 and rs13109270 of PCDH7 showed strong association. PCDH7 has been suggested to play a role in cochlear and amygdaloid complexes. Functional class analysis showed that inner ear and schizophrenia-related genes were enriched inside the linked regions. This study is the first to show the importance of auditory pathway genes in musical aptitude.

A novel mutation W388X underlying properdin deficiency in a Finnish family.

Properdin deficiency is a rare immunological disorder inherited as an X-chromosomal recessive trait. Properdin deficiency poses a significant risk for severe meningococcal infections. About 20 mutations have been reported to underlie properdin deficiency. Here we report a large Finnish family with a novel mutation in the properdin gene (CFP). Based on the total absence of properdin activity in a 14-year-old male patient with an infection resembling meningococcal bacteraemia, the coding region and splice sites of the gene were sequenced. The mutation is located in exon 9 and changes guanine to adenine at nucleotide 1164 (c.1164G>A) that causes tryptophan to change to a premature stop codon (W388X). The mother of the patient was shown to be a carrier of the mutation. In total, the mutation was identified in six females and three young males in the family. The mutation must be inherited from the grandfather who had died of an unknown infectious disease. This is the first mutation of the properdin gene identified in Finland.

Novel PORCN mutations in focal dermal hypoplasia.

Focal dermal hypoplasia (FDH), Goltz or Goltz-Gorlin syndrome, is an X-linked dominant multisystem disorder characterized primarily by involvement of the skin, skeletal system and eyes. We screened for mutations in the PORCN gene in eight patients of Belgian and Finnish origin with firm clinical suspicion of FDH. First, we performed quantitative PCR (qPCR) analysis to define the copy number at this locus. Next, we sequenced the coding regions and flanking intronic sequences of the PORCN gene. Three de novo mutations were identified in our patients with FDH: a 150-kb deletion removing six genes including PORCN, as defined by qPCR and X-array-CGH, and two heterozygous missense mutations; c.992T>G (p.L331R) in exon 11 and c.1094G>A (p.R365Q) in exon 13 of the gene. Both point mutations changed highly conserved amino acids and were not found in 300 control X chromosomes. The three patients in whom mutations were identified all present with characteristic dermal findings together with limb manifestations, which were not seen in our mutation-negative patients. The clinical characteristics of our patients with PORCN mutations were compared with the previously reported mutation-positive cases. In this report, we summarize the literature on PORCN mutations and associated phenotypes.

Effect of mifepristone on the corpus luteum in early pregnancy.

OBJECTIVE: The antiprogestin mifepristone is widely used for medical termination of pregnancy (TOP). Previous studies have suggested that the mechanism of mifepristone is based on its action in the endometrium and myometrium. The aim of this study was to evaluate the possible effects of mifepristone on corpus luteum activity. METHODS: This was a prospective, longitudinal controlled study to which 20 patients undergoing medical TOP (study group) and 20 patients with normal ongoing pregnancy (control group) were recruited. Medical TOP was induced with 200 mg of mifepristone followed by 0.8 mg of misoprostol 2 days later. Three-dimensional ultrasound examinations and hormone assays (progesterone, human chorionic gonadotropin, and 17-hydroxyprogesterone) were performed in both groups on the day of, and 2 days after, administration of mifepristone. Total volume (vascularized + non-vascularized) of the dominant (containing corpus luteum) and non-dominant ovary and serum hormone levels were measured. RESULTS: After administration of mifepristone, a decrease in serum progesterone levels was observed with a simultaneous decrease in the non-vascularized volume of the dominant ovary in the study group. No such changes were observed in the control group. CONCLUSIONS: The observations indicate that, in addition to trophoblastic tissue, the corpus luteum is also the target of mifepristone.

Genome-wide linkage scan for loci of musical aptitude in Finnish families: evidence for a major locus at 4q22.

BACKGROUND: Music perception and performance are comprehensive human cognitive functions and thus provide an excellent model system for studying human behaviour and brain function. However, the molecules involved in mediating music perception and performance are so far uncharacterised. OBJECTIVE: To unravel the biological background of music perception, using molecular and statistical genetic approaches. METHODS: 15 Finnish multigenerational families (with a total of 234 family members) were recruited via a nationwide search. The phenotype of all family members was determined using three tests used in defining musical aptitude: a test for auditory structuring ability (Karma Music test; KMT) commonly used in Finland, and the Seashore pitch and time discrimination subtests (SP and ST respectively) used internationally. We calculated heritabilities and performed a genome-wide variance components-based linkage scan using genotype data for 1113 microsatellite markers. RESULTS: The heritability estimates were 42% for KMT, 57% for SP, 21% for ST and 48% for the combined music test scores. Significant evidence of linkage was obtained on chromosome 4q22 (LOD 3.33) and suggestive evidence of linkage at 8q13-21 (LOD 2.29) with the combined music test scores, using variance component linkage analyses. The major contribution of the 4q22 locus was obtained for the KMT (LOD 2.91). Interestingly, a positive LOD score of 1.69 was shown at 18q, a region previously linked to dyslexia (DYX6) using combined music test scores. CONCLUSION: Our results show that there is a genetic contribution to musical aptitude that is likely to be regulated by several predisposing genes or variants.

The T/G 13915 variant upstream of the lactase gene (LCT) is the founder allele of lactase persistence in an urban Saudi population.

BACKGROUND: The prevalence of lactase persistence is high in Saudi Arabia. OBJECTIVE: To identify a DNA variant for the lactase persistence/non-persistence trait in adult Arabs in Saudi Arabia. METHODS: We sequenced DNA from 432 anonymous neonatal blood donors from five different regions of Saudi Arabia to cover the 400 bp region surrounding the previously identified lactase persistence/non-persistence variant C/T-13910 residing in intron 13 of the MCM6 gene. RESULTS: Two anonymous blood donors carried the C/T-13910 genotype. One variant, T/G -13915, residing 5 bp upstream of the C/T-13910 variant, was present in 332 of 432 (76.9%) of the neonatal samples, compatible with previous prevalence figures of lactase persistence in urban Saudi populations. Determination of disaccharidase activities in 25 intestinal biopsy samples showed a highly significant correlation between lactase activity and the T/G-13915 genotypes (p<0.001; Fisher exact test) as well as between the L:S ratio and the aforementioned genotypes (p<0.001; Fisher exact test). CONCLUSION: The T/G-13915 variant is the founder mutation of lactase persistence in an urban Saudi population. The results obtained here have implications for genetic testing of adult-type hypolactasia and to analysis of human evolution, the origin of cattle domestication and migrations of the populations in the Arabian peninsula.

Juvenile-onset neuronal ceroid lipofuscinosis with infantile CLN1 mutation and palmitoyl-protein thioesterase deficiency.

Accurate diagnosis, especially in progressive hereditary diseases, is essential for the treatment and genetic counseling of the patient and the family. Neuronal ceroid lipofuscinoses (NCL) are amongst the most common groups of neurodegenerative diseases. Infantile, juvenile, and adult-onset types with multiple genotype-phenotype associations have been described. A fluorimetric enzyme assay for palmitoyl protein thioesterase (PPT) from leukocytes and fibroblasts has been previously developed to confirm the diagnosis of infantile NCL. We describe a patient with juvenile-onset NCL phenotype with a new CLN1 mutation and deficient PPT activity. Over 40 different mutations have been found in patients with PPT deficiency, indicating that screening for known mutations is not an efficient way to diagnose this disorder. Therefore, PPT enzyme analysis should precede mutation analysis in suspected PPT deficiency, particularly in patients with granular osmiophilic deposits (GROD) or in patients who have negative ultrastructural data. The use of enzyme assay led to the diagnosis of this patient with juvenile-onset Finnish variant NCL with PPT deficiency, and we expect that greater awareness of the utility of the enzymatic assay may lead to identification of other similar cases awaiting a definitive diagnosis.

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

BACKGROUND: Asperger syndrome is characterised by abnormalities in social interaction as well as repetitive and stereotyped behaviours and interests. The trait is thought to display complex inheritance, but in a subset of families the inheritance resembles the autosomal dominant model. Linkage to 3p14-24 has recently been reported in Asperger syndrome in Finnish families with a maximum multipoint NPL(all) of 3.32 at D3S2432. METHODS: We have replicated linkage findings to 3p21-24 in 12 new extended Asperger syndrome families. Linkage analyses were performed separately for the 12 new families, and linkage and association analyses were also performed jointly with data from the original genome-wide screen. RESULTS: Best two point and multipoint logarithm of the odds (LOD) scores in analyses of both data sets were obtained at D3S2432 (NPL(all) = 3.83) with both subsets of families contributing to linkage. Association analysis of the combined data set produced a trend towards association with D3S2432 and D3S1619. CONCLUSIONS: This study further validates 3q21-24 as a candidate region for Asperger syndrome.

The effect of complement factor H Y402H polymorphism on the outcome of photodynamic therapy in age-related macular degeneration.

PURPOSE: Photodynamic therapy (PDT) has been widely used in the treatment of age-related macular degeneration (AMD). The complement cascade has an important role in the tissue reactions occurring after PDT. The Y402H polymorphism of the complement factor H (CFH) gene has been identified as a risk factor for AMD. Since CFH is central in the regulation of the complement system the authors wanted to analyze whether the CFH Y402H polymorphism modifies the PDT outcome in AMD. METHODS: A total of 88 patients having been treated with PDT and without further scheduled PDT sessions were analyzed. Depending on the situation at their final PDT session the patients were classified retrospectively as PDT-responders or PDT-nonresponders. All patients were genotyped for the CFH Y402H polymorphism. RESULTS: The proportion of PDT-responders was 18/26 (69.2%) in patients homozygous for the CFH Y402H risk allele, 34/50 (68.0%) in heterozygous, and 7/12 (58.3%) in patients with the normal genotype (p=0.520). The median number of PDT treatments of the PDT-responders was three for all the genotypes. CONCLUSIONS: The dysfunction of the CFH related to the risk of AMD and caused by the Y402H polymorphism does not modify the outcome of PDT. Genotyping for CFH Y402H cannot be used to select patients for this treatment.

Genetically defined adult-type hypolactasia and self-reported lactose intolerance as risk factors of osteoporosis in Finnish postmenopausal women.

OBJECTIVE: To study the relationships of molecularly defined lactose malabsorption (LM) and self-reported lactose intolerance (LI) to bone mineral density (BMD) and fractures among Finnish postmenopausal women. DESIGN: A cross-sectional study of two cohorts. SETTING: Helsinki University Central Hospital. SUBJECTS: One cohort was population-based and comprised 453 women, aged 62-78 (mean 69) y. Another comprised 52 women, aged 69-85 (mean 75) y, with osteoporotic fractures and 59 control women, aged 69-83 (mean 74) y, without osteoporosis. METHODS: A single nucleotide polymorphism of the lactase (LCT) gene at chromosome 2q21-22 was studied. It shows complete association with intestinal disaccharidase activity, with the genotype CC(-13 910) meaning adult-type hypolactasia (primary LM) and the genotypes CT(-13 910) and TT(-13 910) lactose absorption. BMD of the heel was measured by dual-energy X-ray absorptiometry (DXA). RESULTS: In the population-based cohort, 16.0% of women had self-reported LI but only 15.3% of them had the CC(-13 910) genotype. Calcium intake from dairy products (P = 0.10) and BMD, adjusted for age, weight, height, exercise, smoking, and estrogen use (P = 0.71) were similar for the genotypes. Women with self-reported LI had reduced calcium intake from dairy products (P < 0.0001) but they were more frequent users of calcium supplements than lactose-tolerants (P < 0.0001). Adjusted BMD was similar for lactose intolerant and tolerant women (P = 0.60). Of 104 women with previous fracture in the population-based cohort, 13.5% had the CC(-13 910) genotype, which did not differ from the prevalence of 19.3% among 347 women without fractures (P = 0.29). The frequency of the CC(-13 910) genotype (23.1%) for 52 women with established osteoporosis was similar as for 59 control women (15.3%) (P = 0.19). CONCLUSION: Molecularly defined LM and self-reported LI are not risk factors for osteoporosis, if calcium intake from diet and/or supplements remains sufficient. Our study confirms the poor correlation between self-reported LI and LM established by different techniques.

A single PCR marker in strong allelic association with the infantile form of neuronal ceroid lipofuscinosis facilitates reliable prenatal diagnostics and disease carrier identification.

The infantile form of neuronal ceroid lipofuscinosis (INCL) is a progressive encephalopathy in children < 2 years old. The disease is one of the Finnish diseases, enriched in this genetically isolated population. The gene responsible for INCL has been recently assigned to the short arm of human chromosome 1. Here we describe DNA-based prenatal and carrier diagnostics using a highly polymorphic marker (HY-TM1) which demonstrates a strong allelic association to the disease locus. 88% of Finnish INCL patients were observed to have the same affected genotype, suggesting that one major CLN1 mutation is enriched in this population. In contrast, all the non-Finnish INCL patients had different allele combinations.

Phenotype-genotype correlation in eight patients with Finnish variant late infantile NCL (CLN5).

The authors analyzed the clinical phenotype, including MRI, of eight patients with Finnish variant late infantile neuronal ceroid lipofuscinosis (vLINCLFin; CLN5; MIM256731). Although the four known mutations, including one novel mutation identified in this study, have very different consequences for the predicted polypeptide, none of them results in an atypical phenotype, as has been reported in other forms of NCL. Thus, it seems likely that each mutation severely disturbs the normal function of the CLN5 protein.

MECP2 gene analysis in classical Rett syndrome and in patients with Rett-like features.

OBJECTIVE: To discuss the diagnostic criteria for Rett syndrome based on mutational screening of the methyl-CpG-binding protein 2 gene ( MECP2 ) in patients with classic Rett syndrome and patients with Rett-like features. METHODS: Thirty-nine patients with classical Rett syndrome, one with preserved speech variant (PSV), and 12 patients with developmental delay and some features of Rett syndrome were recruited for sequence analysis of the MECP2 gene coding region. The phenotype of the patients was correlated with the presence and type of the mutation as well as the X-chromosome inactivation (XCI) pattern. RESULTS: found in 100% of the patients with classical Rett syndrome originating from Finland. One novel mutation, P127L, was detected in a patient with PSV. No mutations were found in other cases. The XCI status was found to be random in 72% of the patients with classical Rett syndrome, including the patient with PSV and all patients with developmental delay informative for the analysis. CONCLUSIONS: An MECP2 mutation can be found in almost every patient with classical Rett syndrome. More patients need to be analyzed in order to clarify the mutation prevalence in patients with atypical Rett syndrome and in patients with mental retardation.

Delayed classic and protracted phenotypes of compound heterozygous juvenile neuronal ceroid lipofuscinosis.

OBJECTIVE: To correlate the phenotypes with the genotypes of 10 Finnish juvenile neuronal ceroid lipofuscinosis (JNCL; late-onset Batten disease) patients who all are compound heterozygotes for the major 1.02-kb deletion in the CLN3 gene. METHODS: The mutations on the non-1.02-kb deletion chromosomes were screened in 6 patients; in the other 4 patients the mutations were known (one affecting a splice site, two missense mutations, and one deletion of exons 10 through 13). Clinical features were examined, and MRI, MRS, somatosensory evoked magnetic field (SEF), and overnight polysomnography (PSG) studies were performed. RESULTS: A novel deletion of exons 10 through 13 was found in 6 patients belonging to three families. In the patients carrying the deletions of exons 10 through 13 the clinical course of the disease was fairly similar. Variation was greatest in the time course to blindness. In these patients the mental and motor decline was slower than in classic JNCL, but more severe than in the two patients with missense mutations in exons 11 and 13. MRI showed brain atrophy in 4 patients. One patient had hyperintense periventricular white matter, otherwise brain signal intensities were normal. SEFs were enhanced in patients older than 14 years, whereas in PSG all but the youngest 6-year-old patient showed epileptiform activity in slow-wave sleep. CONCLUSIONS: JNCL can manifest as at least three different phenotypes: classic, delayed classic, and protracted JNCL with predominantly ocular symptoms. Finnish compound heterozygotes have the delayed classic or the protracted form of JNCL.

Linkage map of the chromosomal region surrounding the infantile neuronal ceroid lipofuscinosis on 1p.

The neuronal ceroid lipofuscinoses (NCLs) of childhood are divided into 3 main types according to age-of-onset, clinical course, and neurophysiological and neuropathological findings: infantile, late infantile, and juvenile. All forms are inherited as an autosomal recessive trait, and their biochemical background is still unknown. The infantile type (INCL) with the earliest age-of-onset and the most severe clinical course, occurs in Finland with an incidence of 1:20,000, i.e., 116 patients have been found in our country up to now, whereas only about 50 cases have been reported from other parts of the world. Earlier we reported the linkage of INCL to the short arm of chromosome 1. Here we describe a more precise linkage map of this area. Our current map places the INCL mutation between D1S57 and D1S79; D1S7 has so far shown no recombination events between the marker and the disease (lod score 4.55 at theta = 0.00). Our material includes 64% of all living patients in Finland, and no linkage disequilibrium of haplotypes is seen, using the 2 physically close markers D1S57 and D1S79. This finding as well as our LINKMAP analyses suggest that the distance between the disease locus and the flanking markers is about 3-4 cm.

Interstitial deletion of bands 11q21-->22.3 in a three-year-old girl defined using fluorescence in situ hybridization on metaphase chromosomes.

A 3-year-old girl has a de novo deletion of 11q21-22.3. The patient was studied because of minor anomalies, disproportionate short stature, and developmental delay. The deletion was first detected by conventional cytogenetic analysis and defined further by using chromosome 11-specific YAC clones by fluorescent in situ hybridization (FISH) on metaphase chromosomes. Three YAC clones, 11H7, 4A5, and IH4, were lacking from one of the patient's chromosome 11. Trigonocepahly, hypertelorism, apparently low-set ears, mild renal abnormality, and delay in speech development found in our patient are similar findings in other published interstitial deletion cases. Our study shows that a molecular cytogenetic approach is useful in defining the specific location and the extent of an interstitial deletion in cytogenetically difficult areas such as 11q.

Physical map of the region containing the gene for Batten disease (CLN3).

CLN3 has been mapped genetically to 16p12, to the interval between D16S288 and D16S383, a sex-averaged genetic distance of 2.1 cM. Analysis of disease haplotypes for four microsatellite markers in this interval, D16S288, D16S299, D16S298, and SPN, has shown significant allelic association between one allele at each of these loci and CLN3. All four of the associated markers were used as nucleation sites in the isolation of genomic clones (YACs). A contig was assembled which contains 3 of the 4 associated markers and which confirmed the relative order of these markers. Marker D16S272 has been located on the physical map between D16S288 and D16S299. Restriction mapping has demonstrated the location of possible CpG islands. One gene, STP, has been localised on the YAC contig proximal to D16S298 and is therefore a candidate for CLN3. Other genes, including IL4R, SGLT2, and UQCRC2, have been excluded from this region.

Linkage analysis of late-infantile neuronal ceroid-lipofuscinosis.

The neuronal ceroid-lipofuscinoses (NCL) are a group of neurodegenerative disorders with an autosomal-recessive pattern of inheritance. There are 3 main categories of childhood NCL, namely, infantile, late-infantile, and juvenile NCL. These can be distinguished on the basis of age of onset, clinical course, and histopathology. A number of variant forms of NCL have also been described, and these show symptoms intermediary between the main classical forms. The genes for both the infantile and juvenile forms of NCL have previously been mapped to chromosome areas 1p32 and 16p12, respectively. The gene for late-infantile NCL (LINCL), CLN2, has been excluded from both these loci, but its location is as yet unknown. Recently, CLN5, the gene for the Finnish variant form of LINCL, was mapped to 13q21.1-32. Using the 3 microsatellite markers which were most tightly linked to CLN5, we have excluded CLN2 from this region using a subset of 17 families. Thus, CLN2 represents a fourth distinct genetic locus involved in the pathogenesis of NCL.

New mutations in the neuronal ceroid lipofuscinosis genes.

Thirty-eight mutations and seven polymorphisms have recently been reported in the genes underlying the neuronal ceroid lipofuscinoses (NCLs) including 11 new mutations described here. A total of 114 mutations and 28 polymorphisms have now been described in the five human genes identified which cause NCL. Thirty-eight mutations are recorded for CLN1/PPT; 40 for CLN2/TTP-1, 31 for CLN3, four for CLN5, one for CLN8. Two mutations have been described in animal genes (cln8/mnd, CTSD). All mutations in NCL genes are contained in the NCL Mutation Database (http://www.ucl.ac.uk/NCL).