exomeSuite: Whole exome sequence variant filtering tool for rapid identification of putative disease causing SNVs/indels.

Exome and whole-genome analyses powered by next-generation sequencing (NGS) have become invaluable tools in identifying causal mutations responsible for Mendelian disorders. Given that individual exomes contain several thousand single nucleotide variants and insertions/deletions, it remains a challenge to analyze large numbers of variants from multiple exomes to identify causal alleles associated with inherited conditions. To this end, we have developed user-friendly software that analyzes variant calls from multiple individuals to facilitate identification of causal mutations. The software, termed exomeSuite, filters for putative causative variants of monogenic diseases inherited in one of three forms: dominant, recessive caused by a homozygous variant, or recessive caused by two compound heterozygous variants. In addition, exomeSuite can perform homozygosity mapping and analyze the variant data of multiple unrelated individuals. Here we demonstrate that filtering of variants with exomeSuite reduces datasets to a fraction of a percent of their original size. To the best of our knowledge this is the first freely available software developed to analyze variant data from multiple individuals that rapidly assimilates and filters large data sets based on pattern of inheritance.

Genetics of human cataract.

The pathogenesis of inherited cataracts of all kinds recapitulates the developmental and cell biology of the lens. Just as each novel mutation provides additional information about the structural or functional biology of the affected gene, each newly identified gene provides insight into the developmental and cellular biology of the lens. The set of genes currently known to be associated with cataract is far from complete, especially for age-related cataract, and there is much additional information to be discovered through further genetic studies.

Molecular genetics of human blue cone monochromacy.

Blue cone monochromacy is a rare X-linked disorder of color vision characterized by the absence of both red and green cone sensitivities. In 12 of 12 families carrying this trait, alterations are observed in the red and green visual pigment gene cluster. The alterations fall into two classes. One class arose from the wild type by a two-step pathway consisting of unequal homologous recombination and point mutation. The second class arose by nonhomologous deletion of genomic DNA adjacent to the red and green pigment gene cluster. These deletions define a 579-base pair region that is located 4 kilobases upstream of the red pigment gene and 43 kilobases upstream of the nearest green pigment gene; this 579-base pair region is essential for the activity of both pigment genes.

A new locus for autosomal dominant posterior polar cataract in Moroccan Jews maps to chromosome 14q22-23.

BACKGROUND: Posterior polar cataract is a clinically distinctive opacity located at the back of the lens. It is commonly acquired in age related cataract, and may infrequently occur in pedigrees with congenital cataract. To date, five loci for autosomal dominant congenital posterior polar cataract have been identified. These include two genes, CRYAB and PITX3, on chromosomes 11q and 10q respectively, and three loci with as yet unknown genes on chromosomes 1p, 16q and 20p. PURPOSE: To find the chromosomal location of a gene causing autosomal dominant congenital posterior polar cataract in three Moroccan Jewish families. METHODS: A whole genome scan was performed using microsatellite markers spaced at approximately 10 cM intervals. For fine mapping, five additional microsatellite markers were genotyped. Two-point lod scores were calculated using MLINK software, from the LINKAGE program package. After linkage was established, several positional candidate genes were assessed by PCR based DNA sequencing. RESULTS: The new cataract locus was mapped to an 11.3 cM interval between D14S980 and D14S1069 on chromosome 14q22-23. A maximum two point lod score of 5.19 at theta = 0 was obtained with the markersD14S274. The positional and functional candidate genes SIX1, SIX4, SIX6, OTX2, and ARHJ were excluded as the cause of cataract in these families. CONCLUSION: An as yet unidentified gene associated with posterior polar cataract maps to the long arm of chromosome 14q22-23.

Novel locus for X linked recessive high myopia maps to Xq23-q25 but outside MYP1.

BACKGROUND: High myopia is a common genetic variation in most cases, affecting 1-2% of people, and is the fourth most common disorder causing blindness worldwide. Six autosomal dominant loci and one X-linked recessive locus have been reported, but no genes responsible for high myopia have been identified. OBJECTIVE: To report a Chinese family in which six males presented with high myopia consistent with an X linked recessive trait. RESULTS: Affected individuals shared three common features: high myopia, reduced visual acuity, and fundal changes of high myopia. Protan and deutan were observed in the family, but they did not co-segregate with the high myopia phenotype. X-chromosome-wide linkage analysis mapped the high myopia locus to a 25 cM (14.9 Mb) region on Xq23-q25 between DXS1210 and DXS8057, with maximum two point lod scores at theta = 0 of 2.75 and 2.29 for DXS1001 and DXS8059, respectively. CONCLUSIONS: This new myopia locus is outside the linked region of the first high myopia locus (MYP1). Refinement of the linkage region with additional families and screening candidate genes for mutation may lead to the identification of the defect gene.

Initiation of endogenous messenger RNA translation on hen oviduct polysomes.

The eIF-2A fraction of reticulocyte ribosomal salt wash is capable of maximally stimulating the translation of endogenous messenger RNA by hen oviduct polysomes. The factor increases the initiation of protein synthesis 2--3-fold when measured by the factor-dependent synthesis of NH2-terminal peptides. The addition to these polysomes of elongation factor, EF-1, also increases protein synthesis but at a distinctly different rate and Mg2+ concentration optimum than the eIF-2A fraction. Moreover, there is no stimulation of NH2-terminal peptide synthesis with EF-1 alone. In contrast, all the known initiation factors are required for the translation of exogenous globulin mRNA on oviduct polysomes. Reticulocyte polysomes isolated by an identical procedure to that used for oviduct polysomes or by standard methods also require all the initiation factors for the translation of either endogenous mRNA or exogenous ovalbumin mRNA. Addition of 7-methylguanosine 5'-monophosphate does not inhibit the factor-dependent stimulation of oviduct polysomes except at high concentrations (1.0 mM) indicating that the sites with which 7-methylguanosine 5'-monophosphate normally competes are already occupied. These findings suggest that the messenger RNA remains bound to the oviduct polysomes or initiation factors. Hence the addition of exogenous factors which are involved with mRNA recognition and binding to the ribosome are not required. It has been previously shown that eIF-2A is capable of binding in vitro the initiatior tRNA to an existing Ado-Urd-Gua-40 S complex and initiating protein synthesis when such a complex is present. These present studies indicate that such an initiation complex may exist within the oviduct cell on membrane-associated polysomes. Under these circumstances eIF-2A mediates binding of the initiator tRNA and initiates protein synthesis.

Prenatal diagnosis of dominant and recessive dystrophic epidermolysis bullosa: application and limitations in the use of KF-1 and LH 7:2 monoclonal antibodies and immunofluorescence mapping technique.

Prenatal diagnosis is now possible for junctional and recessive dystrophic forms of epidermolysis bullosa (EB); however, there is no similar published experience for dominant dystrophic EB, although data with KF-1 monoclonal antibody suggests that both forms of dystrophic EB can be identified at least postnatally with this unique probe. We now report our experience with light microscopy, electron microscopy, immunofluorescence mapping, and KF-1 and LH 7:2 monoclonal antibodies, in both a mother with dominant dystrophic EB and her fetus at risk, and in a fetus previously shown to be affected with recessive dystrophic EB. KF-1 and LH 7:2 antigens were absent in recessive dystrophic EB fetal skin, identical to findings observed postnatally. LH 7:2 was normally expressed in a mother with dominant dystrophic EB and in her fetus at risk for this disease. In contrast, while KF-1 antigen was abnormally expressed in the affected mother, it was normally expressed in only 1/7 fetal biopsies despite the fact that this fetus was shown by light and electron microscopy and immunofluorescence mapping to be unaffected with dominant dystrophic EB. We conclude that 1) transmission electron microscopy can be used to prenatally exclude the diagnosis of dominant dystrophic EB (Cockayne-Touraine variety), 2) immunofluorescence mapping is an accurate technique for prenatal as well as postnatal diagnosis of EB, and 3) KF-1 cannot by itself be used as an accurate probe for the prenatal diagnosis of dominant dystrophic EB, due to the apparent variability in the time for the normal expression of KF-1 in fetal skin during the second trimester.

Localization of cells containing LHRH-like mRNA in rat forebrain using in situ hybridization.

Using in situ hybridization, we localized cells in the rat forebrain which contain mRNA that hybridizes with a radiolabeled, synthetic oligodeoxyribonucleotide (59-mer) complementary to human LHRH mRNA in the region which includes the coding sequence for the decapeptide. These brain areas have been shown previously to contain immunoreactive LHRH cell bodies.

Carrier diagnosis of Duchenne muscular dystrophy using restriction fragment length polymorphisms.

Molecular probes that are tightly linked to and flank the Duchenne muscular dystrophy (DMD) locus, have been used to characterize DMD mutations and diagnose female carriers. Deletions within the Xp21 region were identified for 8 of 71 families studied. Using both DNA and CK studies, accurate (96 to 98%) carrier or noncarrier diagnoses were made for 51 of 75 females at risk in 24 families with a single affected male. DNA studies resulted in an alteration of predicted risk in 40% of the cases. Recombinant diagnostic methods are useful for carrier detection in families with one or more affected males.

Anticipation in myotonic dystrophy. I. Statistical verification based on clinical and haplotype findings.

To determine whether anticipation in myotonic dystrophy (DM) is a true biologic phenomenon or an artifact of ascertainment bias, we studied 201 members of nine DM kindreds, including 67 individuals with the clinical diagnosis of DM. Of 49 parent-child pairs in which both the parents and the children were clinically affected, the onset of DM occurred in an earlier decade of life in the child than the parent in 44 pairs and in the same decade in five pairs (p < 0.001). To eliminate direct ascertainment bias, we excluded nine pairs involving the index patients. Indirect ascertainment bias due to incomplete penetrance was unlikely, since 55% of the children of DM parents had DM. However, by haplotype analysis of restriction fragment length polymorphisms, we diagnosed DM in one of the 42 asymptomatic children of affected parents and excluded DM in twenty-eight. We estimated that patients with early-onset DM would have produced an additional 25 DM children if they had normal fertility and nuptiality. Assuming that the expected age-of-onset distribution occurs without anticipation in these 25, only seven would have had the onset of DM earlier than their parents. With the corrected result, the child would have been affected earlier than the parent in 53 pairs, and the parent would have been affected at the same age as or earlier than the child in 13 pairs (p < 0.001). Thus, the observed anticipation is unlikely to be totally attributable to ascertainment bias, suggesting the potential importance of biologic mechanisms.

Glutathione S-transferase M1 genotype and age-related cataracts. Lack of association in an Italian population.

PURPOSE: To investigate possible associations between the gene number and allelic forms of glutathione S-transferase M1 (GSTM1) and the occurrence of nucleic and cortical age-related cataracts. METHODS: Patients with cortical cataract, nuclear cataract, mixed and cortical cataract, and no cataract were sytematically selected from subjects evaluated in the Italian-American Study of the Natural History of Age-Related Cataract. The patients were typed for the A, B, and null alleles of GSTM1 using a variation of the amplification refractory mutation system. RESULTS: Forty-nine percent of patients (50/102) with cortical cataracts, 45% (13/29) with nuclear cataracts, 51% (36/71) with mixed nuclear and cortical cataracts, and 50% of controls (49/98) were homozygous for the null GSTM1 allele. Twenty-five percent of patients (26/102) with cortical cataracts, 24% (7/29) with nuclear cataracts, 31% with mixed nuclear and cortical cataracts, and 27% of controls (26/98) displayed only the A allele for GSTM1. Twenty-four percent of patients (24/102) with cortical cataract, 24% (7/29) with nuclear cataracts, 14% (10/71) with mixed nuclear and cortical cataract, and 18% of controls showed only the B allele for GSTM1. Two percent of patients (2/102) with cortical cataracts, 7% (2/29) with nuclear cataracts, 4% (3/71) with mixed nuclear and cortical cataracts, and 5% of controls (5/98) showed both A and B alleles for GSTM1. CONCLUSIONS: No associations between the GSTM1 alleles, including the null allele, and cataracts were detected in this study.

The metabolism of fatty acids in human Bietti crystalline dystrophy.

PURPOSE: To investigate the role of abnormal lipid metabolism in Bietti crystalline dystrophy. METHODS: Cultured human lymphocytes and fibroblasts from patients with Bietti crystalline dystrophy (BCD) were incubated in the presence of [(14)C]18:3n-3 or [(14)C]18:2n-6. Incorporation into the cellular lipid pools and further metabolism by desaturation or elongation were monitored by thin-layer chromatography and HPLC. Results were compared with those in normal control subjects and patients with Wolman disease (WD). RESULTS: Pulse-chase experiments with labeled fatty acids in all groups showed that, after 1 hour, radioactivity was largely confined to the triacylglyceride (TG) and choline phosphoglyceride (CPG) pools. However, after several hours, radioactivity was transferred from the TG and CPG pools, some going to the serine and ethanolamine phosphoglyceride (SPG and EPG) pools. Fibroblasts from all groups showed direct transfer of fatty acids (FAs) into CPG and EPG. Incorporation of labeled FAs into the EPG pool paralleled extensive desaturation and elongation of 18:2n-6 to 22:5n-6 and 18:3n-3 to 22:6n-3. Fibroblasts from patients with WD (a lysosomal acid lipase deficiency characterized by excessive lipid accumulation), showed higher incorporation of 18:2n-6 into TGs than did normal or BCD fibroblasts. Conversely, fibroblasts from patients with BCD showed lower conversion of 18:3n-3, but not of 18:2n-6, into polyunsaturated FAs (PUFAs) than those of normal subjects or patients with WD. This was true for total FAs, CPGs, and EPGs. Similar results were found in both fibroblasts and lymphocytes; however, unlike fibroblasts, lymphocytes from normal subjects showed similar levels of incorporation of FAs into EPGs and CPGs. In contrast, incorporation of 18:3n-3 into EPGs was decreased in lymphocytes from patients with BCD. CONCLUSIONS: BCD is characterized by a lower than normal conversion of FA precursors into n-3 PUFA, whereas there is a higher than normal level of n-6 and n-3 FAs incorporation into TGs in cells from patients with WD. These findings raise the possibility that abnormal lipid metabolism associated with BCD is the result of deficient lipid binding, elongation, or desaturation in contrast to the lysosomal acid lipase deficiency found in Wolman disease.

Congenital 21-hydroxylase deficiency as a new deletion mutation. Detection in a proband during subsequent prenatal diagnosis by HLA typing and DNA analysis.

A child with 21-OH-def whose 9 weeks' pregnant mother was referred for prenatal diagnosis was found upon very careful histocompatibility testing to lack expression of any of his father's HLA antigens on his peripheral blood lymphocytes. The possibility of alternative paternity was considered to be extremely unlikely after additional genetic marker tests. The conclusion that the affected child's disease resulted from inheritance of a maternal CYP21B (21-OH) deletion and a de novo deletion in the paternal chromosome 6 segment that includes both the CYP21B (21-OH) and HLA genes was confirmed by subsequent DNA analysis using 21-OH, C4, DPB, and PCH6 probes. The presence of a heterozygous RFLP for DPB, the absence of a deletion for either CYP21B (21-OH) or C4 genes, and the presence of a paternal HLA antigen haplotype on the fetal cells additionally indicated that the fetus lacked the same deletion and could be predicted to be completely normal.

Fine mapping of the usher syndrome type IC to chromosome 11p14 and identification of flanking markers by haplotype analysis.

PURPOSE: To refine the map position of the Usher syndrome type 1C (USH1C) locus to 11p14-p15.1 in the French-Acadian population settled in Louisiana. METHODS: Linkage and haplotype analysis of Ush1C in the French-Acadian families from southwestern Louisiana was carried out using additional markers known to map to the USH1C interval. Markers localized to 11p were also mapped on the J1 somatic cell hybrid panel. This analysis also helped to localize precisely the USH1C interval. RESULTS: New flanking markers for USH1C have been identified, localizing the USH1C gene to a 1 cM interval between markers D11S1397 and D11S1888. Markers D11S1890 and D11S1888 were placed within the USH1C interval. Analysis of all the markers in the USH1C region flanked by D11S1397 and D11S1888 on the J1 somatic cell hybrid panel localized USH1C to the upper half of chromosome 11p14. CONCLUSION: The Usher Syndrome type 1C gene has been localized to a 1 cM interval between the markers D11S1397 and D11S1888 on chromosome 11p14.

Local microdomain structure in the terminal extensions of betaA3- and betaB2-crystallins.

PURPOSE: Although the crystal structures of the core domains of bovine betaB2-crystallin have been determined and those of other betagamma-crystallins modeled, the positions of the N- and C-termini are not resolvable by X-ray crystallography. Here we model the possible structural organization of the terminal arms of mouse betaA3- and betaB2-crystallins and test this model against the results of partial proteolysis. METHODS: The secondary structure of the terminal extensions was predicted by 3 different methods, one a nearest-neighbor method modified to use overlapping sequence tripeptides. Recombinant betaA3- and betaB2-crystallins were expressed using baculovirus vectors in S. frugiperda Sf9 cells. Crystallins were sequenced by the Edman degradation method. RESULTS: The N-terminal extension of betaB2-crystallin includes a series of hydrophilic residues from Q-11 to Q-9 which have high propensity of a helical conformation. The N-terminal arm of betaA3-crystallin is also predicted to have two helical segments, from Q-24 to E-20 and M-13 to A-12. Partial characterization of the baculovirus extract showed a thiol protease inhibited by leupeptin and E-64. As predicted by the model, recombinant betaB2-crystallin subjected to partial proteolysis was cleaved adjacent to the helical domain, while the N-terminal cleavage site in recombinant betaA3-crystallin was within 1 residue of an interhelical junction. Our model also predicts the products of partial proteolytic degradation of betaB2- and betaA3-crystallins from human, rat, bovine and chicken lenses incubated with the protease m-calpain. CONCLUSIONS: These results suggest the existence of local microdomain structures in the N- and C-terminal extensions of betaA3- and betaB2-crystallins, which appear to be more susceptible to proteolytic degradation in regions adjacent to these putative domains.

Comparison of ultraviolet induced photo-kinetics for lens-derived and recombinant beta-crystallins.

PURPOSE: The photobiology of purified recombinant crystallins has not been studied. Here we examine photo-induced aggregation of purified recombinant mouse betaA3-crystallin (rbetaA3) and compare it with that of betaL-crystallins isolated from bovine lenses. METHODS: rbetaA3-Crystallin was expressed in baculovirus-infected Sf9 cells and purified by ion-exchange and gel-filtration chromatography. Protein solutions (pH 7.4) were irradiated at room temperature using a 308 nm excimer laser and light scattering was registered by attenuation of an unabsorbed beam of red light (670 nm). RESULTS: Irradiation of bovine alpha-crystallin, betaL-crystallin, rbetaA3-crystallin and gammaB-crystallin resulted in formation of insoluble aggregates with subsequent light scattering. Different slopes and threshold energies were observed for light scattering by each of these species. Sensitivity to ultraviolet irradiation induced light scattering as determined from threshold energies varied, with gamma-crystallins showing the greatest sensitivity, the betaL- and rbetaA3-crystallins showing an intermediate sensitivity and alpha-crystallins much less sensitive. Low doses (100 J/cm2) resulted in irreversible formation of water soluble oligomers but no insoluble aggregates as indicated by changes in light transmission. The photo-behavior of rbA3 was similar to mixed betaL-crystallin and different from that of alpha- and gamma-crystallins. CONCLUSIONS: Ultraviolet induced sensitivity of purified recombinant crystallins reflects that of mixed crystallin populations and should provide an indication of the pathogenicity of specific crystallin sequence changes associated with lens aging and hereditary cataract.

Autosomal dominant zonular cataract with sutural opacities is associated with a splice mutation in the betaA3/A1-crystallin gene.

PURPOSE: Congenital cataracts constitute a morphologically and genetically heterogeneous group of diseases that are a major cause of childhood blindness. Autosomal Dominant Zonular Cataracts with Sutural Opacities (CCZS) have been mapped to chromosome 17q11-q12 near the betaA3A1-crystallin gene (CRYBA1). The betaA3A1-crystallin gene was investigated as the causative gene for the cataracts. METHODS: The betaA3/A1-crystallin gene was sequenced in affected and control individuals. Base changes were confirmed and assayed in additional family members and controls using NlaIII restriction digestion of PCR amplified DNA sequences. Base changes were assessed for their effects on splicing by information analysis. RESULTS: The cataracts are associated with a sequence change in the 5' (donor) splice site of intron 3: GC(g->a)tgagt. The sequence change also creates a new NlaIII site. This base change cosegregates with the cataracts in this family, being present in every affected individual. Conversely, this base change was not seen in 140 chromosomes examined in 70 unaffected and unrelated individuals. Information theory mutational analysis shows that the base change lowers the information content of the splice site from 6.0 to -6.8 bits, so that splicing would not be expected to occur at the altered site. CONCLUSIONS: Taken together, these observations suggest that the observed mutation might be causally related to the cataracts in this family.

Familial subepithelial corneal amyloidosis (gelatinous drop-like corneal dystrophy): exclusion of linkage to lactoferrin gene.

PURPOSE: Because corneal tissue with familial subepithelial corneal amyloidosis (FSCA; gelatinous drop-like dystrophy of the cornea) contains lactoferrin the possibility that the FSCA gene was the human lactoferrin (hLF) gene was investigated. Due to contradictory published information we also mapped the hLF gene. METHODS: We mapped the hLF gene using a genomic clone of the entire hLF gene as a probe by fluorescence in situ hybridization (FISH). Utilizing PCR primers that are specific to the hLF gene, we also mapped the hLF via radiation somatic cell hybrid analysis. Linkage of the FSCA gene to the hLF gene was evaluated by genetic linkage analysis using polymorphic markers within and in the vicinity of the hLF gene. RESULTS: The hLF gene mapped to the short arm of chromosome 3 at 3p21. Linkage analysis using polymorphic markers for hLF and haplotype analysis of the 3p21 loci indicates that the FSCA gene is not linked to the 3p21 locus. CONCLUSIONS: The gene for FSCA is not the hLF gene in these families.

Denaturing gradient gel electrophoresis of the alpha 1-antitrypsin gene: application to prenatal diagnosis.

A method for detection of the M and Z alleles of the alpha 1-antitrypsin deficiency (AAT) gene has been developed using denaturing gradient gel electrophoresis (DGGE) of DNA samples amplified in vitro by the polymerase chain reaction. Amplification of the 90 nucleotides surrounding the Z mutation site with concurrent attachment of a 40 bp GC-rich region yields DNA fragments that are easily and quickly separated by DGGE. Results are consistently attained in 1-2 days, making this one of the most rapid method of diagnosis of AAT deficiency to date. Additionally, the analyses are completed entirely without the use of radioactive probes, thus eliminating the problems and precautions that are inherent with the use of 32P. The simplicity and reliability of this technique make it well suited for routine use in diagnostic laboratories.

Diagnostic value of ophthalmologic findings in myotonic dystrophy: comparison with risks calculated by haplotype analysis of closely linked restriction fragment length polymorphisms.

To determine diagnostic value of lens opacities in myotonic dystrophy (DM), we examined 98 at-risk members of 9 DM kindreds. Haplotype analysis of restriction fragment length polymorphisms (RFLPs) using ApoC2, CKMM, and pEFD4.2 supported the diagnosis of DM in 33 and excluded the diagnosis in 51 members. The sensitivities of bilateral iridescent lens opacities, posterior cortical lens opacities, orbicularis oculi weakness, low intraocular pressure, ptosis, and ocular myotonia were 46.7, 50.0, 60.6, 59.3, 51.5, and 3.0%, while their specificities were 100.0, 100.0, 98.0, 94.1, 96.1, and 100.0%, respectively. A peripheral pigmentary degeneration and central macular lesions of retina were not found on indirect fundoscopy. In 86.2% of DM patients, bilateral iridescent lens opacities, posterior cortical lens opacities, or both were present. Unilateral iridescent lens opacities occurred in only 3 of our DM patients, and 2 of non-DM relatives showed a few unilateral iridescent particles. Posterior cortical lens opacities in DM patients always affected both eyes in this series. We conclude that 1) bilateral iridescent lens opacities and posterior cortical lens opacities are highly specific for DM and useful for establishing clinical diagnosis of DM, 2) unilateral iridescent lens opacities are infrequent in DM and are seen in some non-DM members, and 3) ocular myotonia and clinical retinopathies are rare in DM.