Clinical and descriptive genetic study of polydactyly: a Pakistani experience of 313 cases

A novel missense variant located within the zinc finger domain of the GLI3 gene was identified in a Vietnamese pedigree with index finger polydactyly

BACKGROUND

Polydactyly, particularly of the index finger, remains an intriguing anomaly for which no specific gene or locus has been definitively linked to this phenotype. In this study, we conducted an investigation of a three-generation family displaying index finger polydactyly.

METHODS

Exome sequencing was conducted on the patient, with a filtration to identify potential causal variation. Validation of the obtained variant was conducted by Sanger sequencing, encompassing all family members.

RESULTS

Exome analysis uncovered a novel heterozygous missense variant (c.1482A>T; p.Gln494His) at the zinc finger DNA-binding domain of the GLI3 protein within the proband and all affected family members. Remarkably, the variant was absent in unaffected individuals within the pedigree, underscoring its association with the polydactyly phenotype. Computational analyses revealed that GLI3 p.Gln494His impacts a residue that is highly conserved across species.

CONCLUSION

The GLI3 zinc finger DNA-binding region is an essential part of the Sonic hedgehog signaling pathway, orchestrating crucial aspects of embryonic development through the regulation of target gene expression. This novel finding not only contributes valuable insights into the molecular pathways governing polydactyly during embryonic development but also has the potential to enhance diagnostic and screening capabilities for this condition in clinical settings.

Prenatal Detection of Novel Compound Heterozygous Splice Site Variants of the KIAA0825 Gene in a Fetus with Postaxial Polydactyly Type A

Postaxial polydactyly (PAP) is a common abnormality characterized by extra digits on hands and/or feet. To date, sequence variants in seven genes have been identified in non-syndromic PAP. In the present study, a fetus manifesting non-syndromic postaxial polydactyly type A (PAPA) was found by fetal ultrasonography. To better evaluate fetal prognosis, SNP array analysis and trio whole-exome sequencing (trio-WES) were performed to identify the underlying etiology. Although SNP array analysis revealed no abnormality, trio-WES identified compound heterozygous splice site variants in KIAA0825, c.-1-2A>T and c.2247-2A>G in intron 2 and intron 12, respectively. These two splice site variants were absent in control databases and were predicted to influence splicing by in silico analysis. To confirm the potential pathogenicity of the variants, in vitro splicing assays using minigene and RNA from peripheral leukocytes of the heterozygous parents were conducted. Minigene and RT-PCR assays demonstrated that the c.-1-2A>T variant led to the loss of the initiation codon, and the c.2247-2A>G variant mainly resulted in exon 13 skipping. Prenatal WES and subsequent functional studies are important approaches for defining the genetic etiology of fetuses with PAPA and are also essential for accurate genetic counseling and decision making. Taken together, this study expands the spectrum of KIAA0825 variations in PAPA patients and increases the knowledge of the molecular consequences of KIAA0825 splice site variants.

Identification of the genetic basis of sporadic polydactyly in China by targeted sequencing

Purpose

Polydactyly is a highly heterogeneous group of skeletal deformities in clinical and genetic background. The variation spectrum in Chinese sporadic polydactyly has not been comprehensively analyzed. To elucidate genetic variation spectrum and genotype-phenotype correlations in Chinese patients with polydactyly, we conducted comprehensive genetic analysis of patients nationwide using targeted sequencing.

Methods

A total of 181 patients diagnosed with polydactylies were recruited. We designed a targeted capture panel for sequencing 721 genes that are associated with the pathogenesis of skeletal dysplasia. We performed rigorous variant- and gene-level filtrations to identify potentially damaging variants, followed by enrichment analysis and gene prioritization.

Results

A total of 568 deleterious variants of 293 genes were identified in 173 of 181 patients with a positive rate of 95.6% by targeted sequencing. For each sample, an average of 3.17 deleterious variants were identified. Especially, 14 pathogenic or likely pathogenic variants were identified in 10 genes in 14 patients out of the 181 patients, providing a positive molecular diagnostic rate of 7.7%.

Conclusion

Targeted sequencing analysis provides a high efficiency approach for the genetic diagnosis of polydactyly. This is the largest next generation sequencing study performed to date in patients with polydactyly and represents the genetic basis of polydactyly typically encountered in genetics clinics.

A Frameshift Variant in KIAA0825 Causes Postaxial Polydactyly

Postaxial polydactyly (PAP) is characterized by counterproductive 5th digit (pinky finger) duplication on hands and/or feet which often leads to functional complications. To date, at least 11 genes involved in causing various types of nonsyndromic polydactylies have been reported. In the present study, a consanguineous family of Sindhi origin with a segregating nonsyndromic form of PAP in an autosomal recessive manner was clinically and genetically evaluated. Genotyping, using polymorphic microsatellite markers, established linkage in the family on chromosome 5q15 harboring the KIAA0825 gene (MIM 617266). Sequence analysis of the gene revealed a novel frameshift variant leading to a premature stop codon [c.143delG, p.(Cys48Serfs*28)]. This is only the 4th novel variant in the KIAA0825 gene that leads to PAP type A10 (PAPA10) (MIM 618498). Identification of variants in the PAP causative gene will support the diagnosis of patients with limb malformations in the Pakistani population.

Clinical Characteristics and Distribution of Thumb Polydactyly in South China: A Retrospective Analysis of 483 Hands

PURPOSE

This study was intended to characterize the epidemiological features of thumb polydactyly (TP) in South China.

METHODS

Clinical records were retrieved from 1 central hospital in South China to identify the patients with a definite diagnosis of TP from January 2004 to January 2017. The cases were classified by their x-ray appearance. The data collected included sex, age at first operation, reoperation, family history, unilateral/bilateral polydactyly, right/left hand involvement in unilateral cases, classification of polydactyly, and the presence of associated congenital anomalies.

RESULTS

A total of 428 patients with a definite diagnosis of TP were identified (278 males and 150 females) involving 483 cases, 373 unilateral and 55 bilateral. A syndrome or associated congenital anomaly was found in 26 (18 unilateral and 8 bilateral cases). A dominant thumb, larger and more developed, was observed in 448 hands (93%), and was the ulnar thumb in 433. Owing to postoperative complications, 31 thumbs (6.4%) underwent reoperation. The average interval from initial surgery to reoperation was 4.8 years.

CONCLUSIONS

Thumb polydactyly had a male predominance in this Chinese cohort, mostly occurring on the right hand with an ulnar dominant thumb. Bilateral cases had a higher incidence of associated anomaly and positive family history than unilateral cases. The need for additional surgery for TP might occur as late as 4.8 years after primary surgery.

TYPE OF STUDY/LEVEL OF EVIDENCE

Therapeutic IV.

Novel IQCE variations confirm its role in postaxial polydactyly and cause ciliary defect phenotype in zebrafish

Polydactyly is one of the most frequent inherited defects of the limbs characterized by supernumerary digits and high-genetic heterogeneity. Among the many genes involved, either in isolated or syndromic forms, eight have been implicated in postaxial polydactyly (PAP). Among those, IQCE has been recently identified in a single consanguineous family. Using whole-exome sequencing in patients with uncharacterized ciliopathies, including PAP, we identified three families with biallelic pathogenic variations in IQCE. Interestingly, the c.895_904del (p.Val301Serfs*8) was found in all families without sharing a common haplotype, suggesting a recurrent mechanism. Moreover, in two families, the systemic phenotype could be explained by additional pathogenic variants in known genes (TULP1, ATP6V1B1). RNA expression analysis on patients' fibroblasts confirms that the dysfunction of IQCE leads to the dysregulation of genes associated with the hedgehog-signaling pathway, and zebrafish experiments demonstrate a full spectrum of phenotypes linked to defective cilia: Body curvature, kidney cysts, left-right asymmetry, misdirected cilia in the pronephric duct, and retinal defects. In conclusion, we identified three additional families confirming IQCE as a nonsyndromic PAP gene. Our data emphasize the importance of taking into account the complete set of variations of each individual, as each clinical presentation could finally be explained by multiple genes.

Variants in KIAA0825 underlie autosomal recessive postaxial polydactyly

Postaxial polydactyly (PAP) is a common limb malformation that often leads to cosmetic and functional complications. Molecular evaluation of polydactyly can serve as a tool to elucidate genetic and signaling pathways that regulate limb development, specifically, the anterior-posterior specification of the limb. To date, only five genes have been identified for nonsyndromic PAP: FAM92A, GLI1, GLI3, IQCE and ZNF141. In this study, two Pakistani multiplex consanguineous families with autosomal recessive nonsyndromic PAP were clinically and molecularly evaluated. From both pedigrees, a DNA sample from an affected member underwent exome sequencing. In each family, we identified a segregating frameshift (c.591dupA [p.(Q198Tfs*21)]) and nonsense variant (c.2173A > T [p.(K725*)]) in KIAA0825 (also known as C5orf36). Although KIAA0825 encodes a protein of unknown function, it has been demonstrated that its murine ortholog is expressed during limb development. Our data contribute to the establishment of a catalog of genes important in limb patterning, which can aid in diagnosis and obtaining a better understanding of the biology of polydactyly.

Sex-associated preventive effects of low-dose aspirin on obesity and non-alcoholic fatty liver disease in mouse offspring with over-nutrition in utero

Aspirin has been found to diminish hypertriglyceridemia and hyperglycemia in both obese rodents and patients with type 2 diabetes mellitus. We aimed to test whether low-dose aspirin can prevent obesity and the progression of non-alcoholic fatty liver disease (NAFLD) in high-risk subjects. We used offspring mice with maternal over-nutrition as a high-risk model of obesity and NAFLD. The offspring were given postnatal HF-diet and diethylnitrosamine (DEN) to induce obesity and NAFLD, and were treated with or without a low dose of aspirin for 12 weeks (ASP or CTL groups). Aspirin treatment reduced body weight gain, reversed glucose intolerance, and depressed hepatic lipid accumulation in female, but not in male mice. Female mice displayed re-sensitized insulin/Akt signaling and overactivated AMPK signaling, with enhanced level of hepatic PPAR-γ, Glut4, and Glut2, while male mice only enhanced hepatic PPAR-α and PPAR-γ levels. The female ASP mice had inhibited p44/42 MAPK activity and enhanced Pten expression, while male displayed activated p38 MAPK signaling. Furthermore, the female but not the male ASP mice reduced Wnt-signaling activity via both the epigenetic regulation of Apc expression and the post-transcriptional regulation of β-catenin degradation. In summary, our study demonstrates a sex-associated effect of low-dose aspirin on obesity and NAFLD prevention in female but not in male mice.

Clinical Genetics of Polydactyly: An Updated Review

Polydactyly, also known as hyperdactyly or hexadactyly is the most common hereditary limb anomaly characterized by extra fingers or toes, with various associated morphologic phenotypes as part of a syndrome (syndromic polydactyly) or may occur as a separate event (non-syndromic polydactyly). Broadly, the non-syndromic polydactyly has been classified into three types, i.e.; preaxial polydactyly (radial), central polydactyly (axial), and postaxial polydactyly (ulnar). Mostly inherited as an autosomal dominant entity with variable penetrance and caused by defects that occur in the anterior-posterior patterning of limb development. In humans, to-date at least 10 loci and six genes causing non-syndromic polydactyly have been identified, including the ZNF141, GLI3, MIPOL1, IQCE, PITX1, and the GLI1. In the present review, clinical, genetic and molecular characterization of the polydactyly types has been presented including the recent genes and loci identified for non-syndromic polydactyly. This review provides an overview of the complex genetic mechanism underlie polydactyly and might help in genetic counseling and quick molecular diagnosis.

Exome sequencing revealed a splice site variant in the IQCE gene underlying post-axial polydactyly type A restricted to lower limb

Polydactyly is characterized by an extra supernumerary digit/toe with or without bony element. To date variants in four genes GLI3, ZNF141, MIPOL1 and PITX1 have been implicated in developing non-syndromic form of polydactyly. The present study involved characterization of large consanguineous family of Pakistani origin segregating post-axial polydactyly type A, restricted to lower limb, in autosomal recessive pattern. DNA of two affected members in the family was subjected to exome sequencing. Sanger sequencing was then followed to validate segregation of the variants in the family members. A homozygous splice acceptor site variant (c.395-1G>A) was identified in the IQCE gene, which completely co-segregated with post-axial polydactyly phenotype within the family. The homozygous variant was absent in different public variant databases, 7000 in-house exomes, 130 exomes from unrelated Pakistani individuals and 215 ethnically matched controls. Mini-gene splicing assay was used to test effect of the variant on function of the gene. The assay revealed loss of first nucleotide of exon 6, producing a -1 frameshift and a premature stop codon 22 bases downstream of the variant (p.Gly132Valfs*22). The study provided the first evidence of involvement of the IQCE gene in limbs development in humans.

Mutational screening of GLI3, SHH, preZRS, and ZRS in 102 Chinese children with nonsyndromic polydactyly

BACKGROUND

Polydactyly is a group of congenital limb malformations that show high degree of phenotypic variability and genetic heterogeneity.

RESULTS

In the present study, four genomic regions (exons of GLI3, SHH, and noncoding sequences of preZRS and ZRS) involved in hedgehog (Hh) signaling pathway were sequenced for 102 unrelated Chinese children with nonsyndromic polydactyly. Two GLI3 variants (c.2844 G > G/A; c.1486C > C/T) and four preZRS variants (chr7:156585336 A>G; chr7:156585421 C>A; chr7: 156585247 G>C; chr7:156585420 A > C) were observed in 2(2.0%) and 6(5.9%) patients, respectively. These variants are not over-represented in the Chinese healthy population. All the 8 cases showed preaxial polydactyly in hands. Additionally, no specific patterns of malformation predicted mutations in other candidate genes or sequences.

CONCLUSIONS

This is the first report of the assessment of the frequency of GLI3/SHH/preZRS/ZRS in Chinese patients to show any higher possibility of mutations or variants for the 4 genes or sequences in China. Developmental Dynamics 246:392-402, 2017. © 2017 Wiley Periodicals, Inc.

Clinical study of 459 polydactyly cases in China, 2010 to 2014

Polydactyly is one of the most common hereditary limb malformations, involving additional digits on the hands and/or feet, which is a very attractive model to appreciate clinical and genetic heterogeneity. A high level of heterogeneity in polydactyly has been identified in different regions. However, such data of the medical literatures for Asian populations are relatively limited. This study was intended to shed light on the phenotypic manifestations of polydactyly in the recruited Chinese population and to characterize the medical literature on this condition. A total of 459 well-characterized polydactyly cases from Shanghai Children's Medical Center were recruited. Their phenotypes, inheritance patterns, and clinical heterogeneity were obtained from clinical medical records. It was found that 4.8% of cases were familial and 95.2% were sporadic. The proportions of preaxial and postaxial polydactyly types were 74.7% and 25.3%, respectively. In preaxial polydactyly, type I formed the overwhelming majority (95.9%). Among the postaxial polydactyly cases, type A was most prevalent at 69.8% and type B was witnessed in 30.2% of cases. Familial and sporadic polydactyly patients mainly had unilateral presentations. A total of 583 limbs with additional digits were recorded in the 459 subjects. Upper limb involvement was more common than lower, and right hand involvement was more common than left for preaxial polydactyly, and lower limb involvement was more common than upper in postaxial polydactyly. This cohort added useful clinical/epidemiological information to the polydactyly literature in the Chinese population and highlighted its marked clinical heterogeneity.

Advances in the molecular genetics of non-syndromic polydactyly

Polydactyly is one of the most common inherited limb abnormalities, characterised by supernumerary fingers or toes. It results from disturbances in the normal programme of the anterior-posterior axis of the developing limb, with diverse aetiology and variable inter- and intra-familial clinical features. Polydactyly can occur as an isolated disorder (non-syndromic polydactyly) or as a part of an anomaly syndrome (syndromic polydactyly). On the basis of the anatomic location of the duplicated digits, non-syndromic polydactyly is divided into three kinds, including preaxial polydactyly, axial polydactyly and postaxial polydactyly. Non-syndromic polydactyly frequently exhibits an autosomal dominant inheritance with variable penetrance. To date, in human, at least ten loci and four disease-causing genes, including the GLI3 gene, the ZNF141 gene, the MIPOL1 gene and the PITX1 gene, have been identified. In this paper, we review clinical features of non-syndromic polydactyly and summarise the recent progress in the molecular genetics, including loci and genes that are responsible for the disorder, the signalling pathways that these genetic factors are involved in, as well as animal models of the disorder. These progresses will improve our understanding of the complex disorder and have implications on genetic counselling such as prenatal diagnosis.

Descriptive epidemiology of hereditary musculoskeletal and limb defects in the isolated population of Chitral, North-West Pakistan

OBJECTIVES

Musculoskeletal and limb defects (MLDs) are the major categories in hereditary anomalies and are a significant source of the disabilities. This study aimed at elucidating the nature and pattern of MLDs prevalent in Chitral district, which is an isolated population in the North-West of Pakistan.

METHODS

A cross-sectional epidemiological study was conducted in Chitral and subjects/families with MLDs were ascertained from public places, hospitals and door-to-door visits. The phenotypic manifestations, expressivity, sporadic/familial presentations, isolated/syndromic nature, inheritance pattern, and socio-demographic attributes, of MLDs were observed.

RESULTS

A total of 153 independent subjects/families with certain types of MLDs were recruited. The MLDs were classified into 9 major and 22 minor entities. In this cohort, polydactyly was observed to be overwhelmingly common (71%), followed by syndactyly and absence limb deformities. The majority of the cases (78%) had sporadic nature, 93% anomalies had isolated presentations; upper limbs were more commonly affected than the lower limbs; and unilateral cases were twice in ratio than bilateral. The majority of the malformations had milder phenotypes, however, 17% of the MLDs were severe in nature and resulted in certain types of disability, compromising the normal life of the subject.

CONCLUSION

This research witnesses a distinctive pattern of MLDs in Chitral, which has not been reported for any other population of Pakistan so far. Further studies are required to observe the molecular etiologies of these malformations and to offer rapid diagnosis and genetic counseling.

Prevalence and pattern of traumatic limb amputations in female population of Bhimber District, Azad Jammu and Kashmir, Pakistan

Objective:

Traumatic limb amputations (TLA) are structural defects that cause mild-to-severe disabilities and have significant impact on the quality of life of subjects. A recent epidemiological study in Bhimber District, AJK, Pakistan, revealed that TLA had a very high incidence among the young/adult females. The present study aimed at determining the prevalence, pattern, causes and risk factors associated with TLA in that female sample.

Methods:

In a prospective door-to-door survey, 1731 females were randomly enrolled, and clinico-etiological investigations on 19 subjects with TLA were carried out in a follow-up study. Affected subjects were physically examined and phenotypic detail and restriction to normal function were documented.

Results:

There were 19 subjects with TLA, hence the prevalence was estimated to be 10.98/1,000 (0.011%; CI=0.0061-0.0159). TLA mostly involved the upper limbs and right hand. Transphalangeal amputations were most frequent, followed by involvements of middle/upper arm and leg segments. These analyses further revealed that agriculture tools were the leading cause of trauma. TLA were witnessed to be higher in subjects originating from Samahni tehsil (OR:2.71), rural areas (OR:3.33), those who were illiterate (OR:2.65), married, spoke Pahari language (OR:1.73), those who fall in higher age category (OR:16.74), and had certain professions.

Conclusion:

Limb amputations had heavy bearings on the lives of subjects. Curiously, majority of these traumas could be avoided by adopting certain safety measures. Prevalence and risk estimate of TLA across various socio-demographic variables of Bhimber population would be useful in guiding further studies and the public health policy to mitigate the impact of these anomalies.

Polydactyly: phenotypes, genetics and classification

Polydactyly is one of the most common hereditary limb malformations featuring additional digits in hands and/or feet. It constituted the highest proportion among the congenital limb defects in various epidemiological surveys. Polydactyly, primarily presenting as an additional pre-axial or post-axial digit of autopod, is a highly heterogeneous condition and depicts broad inter- and intra-familial clinical variability. There is a plethora of polydactyly classification methods reported in the medical literature which approach the heterogeneity in polydactyly in various ways. In this communication, well-characterized, non-syndromic polydactylies in humans are reviewed. The cardinal features, phenotypic variability and molecular advances of each type have been presented. Polydactyly at cellular and developmental levels is mainly a failure in the control of digit number. Interestingly, GLI3 and SHH (ZRS/SHH enhancer), two antagonistic factors known to modulate digit number and identity during development, have also been implicated in polydactyly. Mutations in GLI3 and ZRS/SHH cause overlapping polydactyly phenotypes highlighting shared molecular cascades in the etiology of additional digits, and thus suggesting the lumping of at least six distinct polydactyly entities. However, owing to the extreme phenotypic and clinical heterogeneity witnessed in polydactyly a substantial genetic heterogeneity is expected across different populations and ethnic groups.