@article {772, title = {Cytoplasmic "ciliary inclusions" in isolation are not sufficient for the diagnosis of primary ciliary dyskinesia.}, journal = {Pediatr Pulmonol}, volume = {55}, year = {2020}, month = {2020 01}, pages = {130-135}, abstract = {

BACKGROUND: The diagnosis of primary ciliary dyskinesia (PCD) is difficult and requires a combination of clinical features, nasal nitric oxide testing, cilia ultrastructural analysis by electron microscopy (EM), and genetics. A recently described cytoplasmic ultrastructural change termed "ciliary inclusions" was reported to be diagnostic of PCD; however, no supporting evidence of PCD was provided. In this study, we sought to confirm, or refute, the diagnosis of PCD in subjects with "ciliary inclusions" on EM.

METHODS: Six subjects from five families with previous lab reports of "ciliary inclusions" on EMs of ciliated cells were identified and evaluated at a Genetic Disorders of Mucociliary Clearance Consortium site. We performed a detailed clinical history, nasal nitric oxide measurement, genetic testing including whole-exome sequencing (WES), and when possible, repeat ciliary EM study.

RESULTS: Only one of six subjects had multiple and persistent clinical features congruent with PCD. No subject had situs inversus. Only one of six subjects had a very low nasal nitric oxide level. No "ciliary inclusions" were found in three subjects who had a repeat ciliary EM, and ciliary axonemal ultrastructures were normal. Genetic testing, including WES, was negative for PCD-causing genes, and for pathogenic variants in gene pathways that might cause "ciliary inclusions," such as ciliary biogenesis.

CONCLUSION: "Ciliary Inclusions", in isolation, are not sufficient to diagnosis PCD. If seen, additional studies should be done to pursue an accurate diagnosis.

}, keywords = {Child, Preschool, Cilia, Ciliary Motility Disorders, Female, Genetic Testing, Humans, Infant, Male, Nasal Mucosa, Nitric Oxide, Whole Exome Sequencing}, issn = {1099-0496}, doi = {10.1002/ppul.24528}, author = {Vece, Timothy J and Sagel, Scott D and Zariwala, Maimoona A and Sullivan, Kelli M and Burns, Kimberlie A and Dutcher, Susan K and Yusupov, Roman and Leigh, Margaret W and Knowles, Michael R} } @article {839, title = {Mapping and characterization of structural variation in 17,795 human genomes.}, journal = {Nature}, volume = {583}, year = {2020}, month = {2020 07}, pages = {83-89}, abstract = {

A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and resources for the study of structural variants have lagged behind those for smaller variants. Here we used a scalable pipeline to map and characterize structural variants in 17,795 deeply sequenced human genomes. We publicly release site-frequency data to create the largest, to our knowledge, whole-genome-sequencing-based structural variant resource so far. On average, individuals carry 2.9 rare structural variants that alter coding regions; these variants affect the dosage or structure of 4.2 genes and account for 4.0-11.2\% of rare high-impact coding alleles. Using a computational model, we estimate that structural variants account for 17.2\% of rare alleles genome-wide, with predicted deleterious effects that are equivalent to loss-of-function coding alleles; approximately 90\% of such structural variants are noncoding deletions (mean 19.1 per genome). We report 158,991 ultra-rare structural variants and show that 2\% of individuals carry ultra-rare megabase-scale structural variants, nearly half of which are balanced or complex rearrangements. Finally, we infer the dosage sensitivity of genes and noncoding elements, and reveal trends that relate to element class and conservation. This work will help to guide the analysis and interpretation of structural variants in the era of whole-genome sequencing.

}, keywords = {Alleles, Case-Control Studies, Continental Population Groups, Epigenesis, Genetic, Female, Gene Dosage, Genetic Variation, Genetics, Population, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Male, Molecular Sequence Annotation, Quantitative Trait Loci, Software, Whole Genome Sequencing}, issn = {1476-4687}, doi = {10.1038/s41586-020-2371-0}, author = {Abel, Haley J and Larson, David E and Regier, Allison A and Chiang, Colby and Das, Indraniel and Kanchi, Krishna L and Layer, Ryan M and Neale, Benjamin M and Salerno, William J and Reeves, Catherine and Buyske, Steven and Matise, Tara C and Muzny, Donna M and Zody, Michael C and Lander, Eric S and Dutcher, Susan K and Stitziel, Nathan O and Hall, Ira M} } @article {807, title = {Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia.}, journal = {PLoS Genet}, volume = {16}, year = {2020}, month = {2020 08}, pages = {e1008691}, abstract = {

Primary ciliary dyskinesia (PCD) is characterized by chronic airway disease, reduced fertility, and randomization of the left/right body axis. It is caused by defects of motile cilia and sperm flagella. We screened a cohort of affected individuals that lack an obvious axonemal defect for pathogenic variants using whole exome capture, next generation sequencing, and bioinformatic analysis assuming an autosomal recessive trait. We identified one subject with an apparently homozygous nonsense variant [(c.1762C>T), p.(Arg588*)] in the uncharacterized CFAP57 gene. Interestingly, the variant results in the skipping of exon 11 (58 amino acids), which may be due to disruption of an exonic splicing enhancer. In normal human nasal epithelial cells, CFAP57 localizes throughout the ciliary axoneme. Nasal cells from the PCD patient express a shorter, mutant version of CFAP57 and the protein is not incorporated into the axoneme. The missing 58 amino acids include portions of WD repeats that may be important for loading onto the intraflagellar transport (IFT) complexes for transport or docking onto the axoneme. A reduced beat frequency and an alteration in ciliary waveform was observed. Knockdown of CFAP57 in human tracheobronchial epithelial cells (hTECs) recapitulates these findings. Phylogenetic analysis showed that CFAP57 is highly conserved in organisms that assemble motile cilia. CFAP57 is allelic with the BOP2/IDA8/FAP57 gene identified previously in Chlamydomonas reinhardtii. Two independent, insertional fap57 Chlamydomonas mutant strains show reduced swimming velocity and altered waveforms. Tandem mass tag (TMT) mass spectroscopy shows that FAP57 is missing, and the "g" inner dyneins (DHC7 and DHC3) and the "d" inner dynein (DHC2) are reduced, but the FAP57 paralog FBB7 is increased. Together, our data identify a homozygous variant in CFAP57 that causes PCD that is likely due to a defect in the inner dynein arm assembly process.

}, keywords = {3T3 Cells, Adult, Animals, Axoneme, Cells, Cultured, Chlamydomonas reinhardtii, Cilia, Ciliary Motility Disorders, Codon, Nonsense, Conserved Sequence, Dyneins, Humans, Male, Mice, Microtubule-Associated Proteins, Plant Proteins, Proteins, Respiratory Mucosa}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1008691}, author = {Bustamante-Marin, Ximena M and Horani, Amjad and Stoyanova, Mihaela and Charng, Wu-Lin and Bottier, Mathieu and Sears, Patrick R and Yin, Wei-Ning and Daniels, Leigh Anne and Bowen, Hailey and Conrad, Donald F and Knowles, Michael R and Ostrowski, Lawrence E and Zariwala, Maimoona A and Dutcher, Susan K} }