Whole Blood from lavender top (EDTA) tube

Peripheral Blood:
For infants under 1 year of age: 1-2 mL in a lavender (EDTA)
For children over 1 year of age: 3-5 mL in a lavender (EDTA)
For adults: 5-7 mL in a lavender (EDTA)

DO NOT FREEZE BLOOD SPECIMENS. Store at 4°C prior to delivery to the lab. Label all tubes with the patient name and medical record number.

Submit specimen to laboratory as soon as possible after collection. DO NOT FREEZE.

After hours specimens should be taken to Specimen Control. For questions after hours, call (319) 356-1616 and ask the operator to page the cytogenetics on-call staff at pager #5525.

Specimens accepted in the lab Monday-Friday, 0800-1700.

Final results within 30 days

Negative

This test detects single nucleotide variants and small insertions or deletions in the protein-coding regions of the human genome. Exome sequencing may be considered for individuals with congenital anomalies, developmental delay, intellectual disability, or other suspected genetic condition.

Exome Sequencing Informed Consent Form

Shivanand R. Patil Cytogenetics & Molecular Laboratory Website

Only coding regions and canonical splice sites are interrogated. Not all exons in the genome can be reliably sequenced by this methodology due to high homology, repetitive and low complexity sequence. Some regions may not have sufficient depth of coverage to identify variants. Certain types of variants are not detected by this test including structural variants, copy number variants, trinucleotide repeat expansions and mitochondrial DNA variants. This test does not reliably detect mosaic variants. Our interpretation is based on the clinical information provided and our current understanding of genes in which variants are identified. Available evidence for variant classification may change over time.

If ACMG secondary findings analysis were requested, pathogenic and likely pathogenic variants in the genes recommended by the ACMG Secondary Findings v3.1 are reported for the proband. The presence or absence of the proband's identified secondary findings is reported for family members submitted for variant interpretation as part of the proband's test. Variants that may be present in the family members but not present in the proband would not be detected. Pathogenic or likely pathogenic variants may be present in a ACMG Secondary Findings gene that is not detectable by this methodology. Absence of reportable variant does not rule out a causative variant in that gene, or variants in other genes that may confer susceptibility to a similar disorder.

References: PMID: 35802134, 25741868, 26931183

Pursuant to the requirements of CLIA'88, the performance of this test has been validated by the University of Iowa Cytogenetics and Molecular Laboratory. It has not been cleared or approved by the U.S. Food and Drug Administration (FDA).

Genomic DNA is extracted directly from submitted specimen. The DNA is prepared using Illumina PCR Free library preparation, following standard protocol as described in manufacturer's instructions (Illumina DNA PCR Free Library Prep Reference Guide). Genomic DNA is sequenced with paired end reads on an Illumina platform. Bi-directional sequencing reads are assembled and aligned to human genome reference sequence build GRCh38/UCSC hg38. Using Emedgene (Illumina) software, data are filtered and analyzed to identify sequence variants in coding exons and canonical splice sites. The expected mean depth of coverage is >=30X. Reported variants are confirmed, if necessary, by an appropriate orthogonal method (dideoxy Sanger DNA sequencing) in the proband. Sequence variants are reported according to the HGVS guidelines. Variants are classified according to ACMG/AMP standards and Guidelines. Variants determined to be benign or likely benign, or variants in genes unlikely to be associated with the described phenotype are not reported.

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