High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses

• Skeletal ciliopathies are a heterogenous group of disorders with overlapping clinical and radiographic features including bone dysplasia and internal abnormalities. To date, pathogenic variants in at least 30 genes, coding for different structural cilia proteins, are reported to cause skeletal ciliopathies. Here, we summarize genetic and phenotypic features of 34 affected individuals from 29 families with skeletal ciliopathies. Molecular diagnostic testing was performed using massively parallel sequencing (MPS) in combination with copy number variant (CNV) analyses and in silico filtering for variants in known skeletal ciliopathy genes. We identified biallelic disease-causing variants in seven genes: DYNC2H1, KIAA0753, WDR19, C2CD3, TTC21B, EVC, and EVC2. Four variants located in non-canonical splice sites of DYNC2H1, EVC, and KIAA0753 led to aberrant splicing that was shown by sequencing of cDNA. Furthermore, CNV analyses showed an intragenic deletion of DYNC2H1 in one individual and a 6.7 Mb de novo deletion on chromosome 1q24q25 in another. In five unsolved cases, MPS was performed in family setting. In one proband we identified a de novo variant in PRKACA and in another we found a homozygous intragenic deletion of IFT74, removing the first coding exon and leading to expression of a shorter message predicted to result in loss of 40 amino acids at the N-terminus. These findings establish IFT74 as a new skeletal ciliopathy gene. In conclusion, combined single nucleotide variant, CNV and cDNA analyses lead to a high yield of genetic diagnoses (90%) in a cohort of patients with skeletal ciliopathies.

Ämnesord

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)

MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Medical Genetics (hsv//eng)

Nyckelord

c2cd3 protein

complementary DNA

dync2h1 protein

evc protein

evc2 protein

genomic DNA

ift74 protein

kiaa0753 protein

protein

ttc21b protein

unclassified drug

wdr19 protein

C2cd3 protein

human

cytoplasmic dynein

cytoskeleton protein

DYNC2H1 protein

human

EVC protein

human

EVC2 protein

human

isoprotein

KIAA0753 protein

human

membrane protein

microtubule associated protein

signal peptide

TTC21B protein

human

WDR19 protein

human

adolescent

adult

amino terminal sequence

Article

asphyxiating thoracic dystrophy

blood sampling

child

chondrodysplasia

chromosome 1q

chromosome 1q24q25

ciliopathy

clinical article

clinical feature

cohort analysis

comparative genomic hybridization

computer model

controlled study

copy number variation

cranioectodermal dysplasia

developmental delay

diagnostic value

DNA extraction

DNA sequencing

DNA splicing

Ellis van Creveld syndrome

exon

female

fetus

fetus lung

gene deletion

gene expression

gene sequence

genetic screening

human

human tissue

infant

Joubert syndrome

lung parenchyma

male

molecular diagnosis

nephronophthisis

newborn

pedigree

phenotype

preschool child

retrospective study

RNA analysis

school child

short rib polydactyly syndrome type 3

single nucleotide polymorphism

skeleton malformation

transcription initiation site

whole exome sequencing

whole genome sequencing

aged

bone dysplasia

genetic predisposition

genetics

high throughput sequencing

human genome

metabolism

middle aged

pathology

skeletal muscle

Bone Diseases

Developmental

Ciliopathies

Cytoplasmic Dyneins

Cytoskeletal Proteins

Genetic Predisposition to Disease

Genome

Human

High-Throughput Nucleotide Sequencing

Humans

Intercellular Signaling Peptides and Proteins

Intracellular Signaling Peptides and Proteins

Membrane Proteins

Microtubule-Associated Proteins

Muscle

Skeletal

Protein Isoforms

Publikations- och innehållstyp

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