Multiplex targeted high‐throughput sequencing in a series of 352 patients with congenital limb malformations

Abstract

Congenital limb malformations (CLM) comprise many conditions affecting limbs and more than 150 associated genes have been reported. Due to this large heterogeneity, a high proportion of patients remains without a molecular diagnosis. In the last two decades, advances in high throughput sequencing have allowed new methodological strategies in clinical practice. Herein, we report the screening of 52 genes/regulatory sequences by multiplex high‐throughput targeted sequencing, in a series of 352 patients affected with various CLM, over a 3‐year period of time. Patients underwent a clinical triage by expert geneticists in CLM. A definitive diagnosis was achieved in 35.2% of patients, the yield varying considerably, depending on the phenotype. We identified 112 single nucleotide variants and 26 copy‐number variations, of which 52 are novel pathogenic or likely pathogenic variants. In 6% of patients, variants of uncertain significance have been found in good candidate genes. We showed that multiplex targeted high‐throughput sequencing works as an efficient and cost‐effective tool in clinical practice for molecular diagnosis of congenital limb malformations. Careful clinical evaluation of patients may maximize the yield of CLM panel testing.

TAR syndrome: Clinical and molecular characterization of a cohort of 26 patients and description of novel noncoding variants of RBM8A

“…We included only cases harboring biallelic variants in RBM8A . Eight of them were reported previously (Jourdain et al, 2020; Table S1). All patients were referred by clinical geneticists or foetopathologists.…”

“…In 2012, Albers et al resolved the complex inheritance mechanism of TAR syndrome and identified the first two noncoding SNPs of RBM8A implicated in this condition (Albers et al, 2012). With the 5′‐UTR and 3′‐UTR variants characterized in this work, we add to the set of known hypomorphic alleles in TAR syndrome, improving the performance of molecular diagnostic in TAR syndrome close to 73% on the basis of our previously reported unbiased cohort (Jourdain et al, 2020). Nevertheless, the exact mechanism by which these SNPs lead to reduced levels of Y14 remains unclear at the present time.…”

Identification of the third FGF9 variant in a girl with multiple synostosis–comparison of the genotype:phenotype of FGF9 variants in humans and mice

“…We reported the second variant, c.184A>G;p.(Arg62Gly) in a father and son with SYNS but they also had craniosynostosis, with the son requiring surgical intervention 5 . This same variant was subsequently observed in another patient with SYNS, but no craniosynostosis was reported 6 . Here, we report the third FGF9 variant, c.427A>T;p.(Asn143Tyr) in a young girl with SYNS.…”

“…To date, only two heterozygous FGF9 variants have been reported in humans with SYNS3, c.296G>A;p.(Ser99Asn) and c.184A>G;p.(Arg62Gly) 3,5,6 . Here, we report a third variant, located at the same amino acid residue as the Eks mouse mutation.…”

“…Pathogenic variants in NOG , GDF5 , FGF9 , and GDF6 account for the four different forms of SYNS (SYNS1‐4, respectively) 1‐4 . SYNS3 (MIM 612961), due to variants in the fibroblast growth factor 9 gene (FGF9) , is characterized by limitation and/or fusion of joints in hands and feet, humeroradial and lumbar joints synostosis, and with or without craniosynostosis 3,5,6 …”