Recurrent rhinovirus infections in a child with inherited MDA5 deficiency

Lamborn, Ian T.; Jing, Huie; Zhang, Yu; Drutman, Scott B.; Abbott, Jordan K.; Munir, Shirin; Bade, Sangeeta; Murdock, Heardley M.; Santos, Celia P.; Brock, Linda G.; Masutani, Evan; Fordjour, Emmanuel Y.; McElwee, Joshua J.; Hughes, Jason D.; Nichols, Dave P.; Belkadi, Aziz; Oler, Andrew J.; Happel, Corinne S.; Matthews, Helen F.; Abel, Laurent; Collins, Peter L.; Subbarao, Kanta; Gelfand, Erwin W.; Ciancanelli, Michael J.; Casanova, Jean-Laurent; Su, Helen C.

Genomic DNA from the patient and family members were isolated from PBMC using the DNeasy kit (QIA GEN). Whole exome sequencing, using SureSelect Human All Exon 50 Mb kit (Agilent Technologies) coupled with massively parallel sequencing by Illumina HiSeq Sequencing System, was performed using 3 µg of genomic DNA collected from patient, both parents, and an unaffected sister. Sequenced DNA reads were mapped to the hg19 human genome reference by Burrows-Wheeler Aligner with default parameters. Single-nucleotide variant and indel calling were performed using the Genome Analysis Toolkit (Broad Institute). All SNVs/indels were annotated by SeattleSeq Annotation, and an in-house custom analysis pipeline was used to filter and prioritize for nonsynonymous and novel/ rare variants (MAF < 0.001) under autosomal recessive or de novo genetic models. UCSC gene sorter Microarray data (GNF Expression Atlas 2 Dta from U133A and GNF1H chips) and Illumina Human BodyMap RNA-seq data were used to prioritize variants for functional validation. For confirmation of IFIH1 mutations and genotyping of the brother, genomic DNA was PCR-amplified using forward primer 5′-CAA TGA CAC AAA TGC CAT CA-3′ and reverse primer 5′-CAG GGA GTG GAA AAA CCA GA-3′. Sanger dideoxy sequencing of purified PCR-amplified products was performed by the Genomics Unit of the Rocky Mountain Laboratories Research Technologies Section of the NIA ID. The WES data were deposited under dbGaP accession no. phs001235.v1.p1.