Consanguinity, prevalence pattern of hereditary malformations, and genetic analyses of rare anomalies segregating in families from Southern Punjab, Pakistan

Abstract

Rahim Yar Khan District is a remote town of Southern Punjab Pakistan with inhabitants of mixed culture and origin. This multi-faceted study was designed in order to, 1): get an insight into the population structure of Rahim Yar Khan district through determining consanguinity and inbreeding coefficient; 2) to observe the prevalence pattern of hereditary and congenital anomalies commonly occurring in the population; 3) to report phenotypic variability in limb deficiency disorders; 4) and to molecularly characterize rare malformations segregating in extended families. First, I conducted an epidemiological survey to collect data about consanguinity prevalence and its relationship with biodemographic parameters. In a cross-sectional approach, first-hand data of 2174 females were obtained and bivariate and multivariate logistic regression analyses were performed. It was observed that Rahim Yar Khan District has a high prevalence of consanguinity, i.e., 58.5% with a cumulative coefficient of inbreeding IC-F=0.0355. Consanguinity showed a significant association with variables like rural origin, Saraiki language, nuclear household and illiteracy. In subjects with consanguineous unions, fertility and mean live births were higher contrasting to category of non-consanguineous unions, but no statistically significant differences were detected in consanguineous couples and non-consanguineous couples regarding child mortality and morbidity. Secondly, a total of 231 independent cases of congenital and hereditary anomalies (HDs) were recruited from Rahim Yar Khan District. An estimated 62.8% cases were sporadic and 37.2% familial; and 82.7% isolated and 17.3% syndromic. HDs were categorized into 12 broad phenotypic categories. Neurological defects (n=65; proportion:0.2814; CI:0.2234-0.3394) topped the list of all anomalies followed by limb anomalies (n=58), musculo-skeletal defects (n=33), deaf/mute cases (n=31), and visual impairments (n=21). Thirdly, eight independent cases with transverse limb defects (TLD) were recruited (case series 1), 7 of which were nonsyndromic and one was syndromic. The anomalies in these subjects exhibited as unilateral amputation through the palm, accompanied with the short or hypoplastic thumb, mild to moderate shortening of the affected limb, distorted palmer creases, and relatively unaffected contralateral limb or feet. Moreover, six independently recruited cases with thumb aplasia are reported (case series 2). All cases had isolated presentation and five subjects had sporadic occurrence. The involved arms of subjects showed the absolute absence of first digital rays, medial inclinations of middle and little fingers, narrowing of palms, absence of small carpals, and reduction in the normal size of zeugopod. Cenani-Lenz syndactyly syndrome (CLSS) is a hereditary condition having phalangeal disorganization with a variable degree of oligodactyly/syndactyly features. Mutations in LRP4 have been implicated in families with CLSS. Two independent Pakistani families with characteristic features of CLSS were recruited. In kindred 1 and 2, one and two affected individuals born to consanguineous couples were observed, respectively. Affected subjects in both families were presented with drastically reduced autopod and zeugopod with grossly disorganized skeletal elements, the features consistent with CLSS spoon-head type. Additionally, affected subjects presented certain anomalous facial features including hypertelorism, down-slanting palpebral fissures and enamel hypoplasia. Mutation analyses revealed a A>G base transition in exon 12 at position c.1820 in LRP4 in the index patients in both families. The mutation segregation was concordant with the disease model in both families. Our study provided a support to genotype-phenotype correlation as a missense mutation caused a relatively milder form of CLS. DuPan syndrome, one of several chondrodysplasias, affect appendicular skeleton without causing any harm in the axial skeleton. It is caused by a member of the BMP family, CDMP1 which regulates condensation and differentiation of mesenchymal tissues during skeletal development in embryonic growth. Another independent limb malformation, Brachydactyly type C (BDC) depict consistent clinical features like brachymesophalangy of second, third and fifth digits, with hyperphalangy of the second and third digits along with short proximal phalanges and reduced anterior metacarpal. An extended family with simultaneous segregation of DuPan syndrome and BDC in various loops of the pedigree was studied. These characteristic phenotypic entities were observed to show clear autosomal recessive and autosomal dominant inheritance patterns, respectively. Molecular genetic analyses of this family demonstrated that a novel mutation NM_000557(GDF5):c.404delC in CDMP1 segregated with the DuPan syndrome and brachydactyly type C phenotypes in homozygous and heterozygous states, respectively. Intellectual disability (ID) is characterized by reduced adaptive and cognitive functionality affecting 3% population worldwide. A large Pakistani family with multiple affected subjects exhibiting the symptoms of inherited ID was studied. Initially, SNP based genotyping was carried out with the help of a commercial service provider. Further, homozygosity mapping was used in order to detect regions of homozygosity shared among the patients. One patient from this family was selected for exome sequencing. Analyses of these data led to the exclusion of many of the previously known genes for ID. Nonsynonymous homozygous variants were identified in four genes which also fall within the homozygous intervals detected in SNP analyses. One of the identified genes has been implicated in autosomal recessive intellectual disability while the rest three are expressed in the brain. Identified variants the currently being tested through Sanger sequencing. In conclusion, this study presents interesting data regarding inbreeding coefficient and clinical and molecular characterization of hereditary anomalies of rare phenotypes