Editors: Donna E. Hansel, MD, PhD, division head of pathology and laboratory medicine, MD Anderson Cancer Center, Houston; James Solomon, MD, PhD, assistant professor, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York; Erica Reinig, MD, assistant professor and medical director of molecular diagnostics, University of Wisconsin-Madison; Marcela Riveros Angel, MD, molecular genetic pathology fellow, Department of Pathology, Oregon Health and Science University, Portland; Maedeh Mohebnasab, MD, assistant professor of pathology, University of Pittsburgh; Alicia Dillard, MD, clinical pathology chief resident, New York-Presbyterian/Weill Cornell Medical Center; and Richard Wong, MD, PhD, assistant professor of pathology, University of California San Diego.
Benefit of routine whole genome sequencing for children with cancer
September 2024—Oncology patients may benefit greatly from whole genome sequencing. Previous studies have suggested that it can provide relevant information pertaining to pediatric cancers, especially in selected cohorts of patients with high-risk disease. However, its clinical utility has not been thoroughly explored in routine clinical practice. The authors of this study examined the benefits of whole genome sequencing (WGS) in a consecutive cohort of pediatric patients from two institutions who required molecular workup for hematological neoplasms and solid tumors. Great Ormond Street Hospital, London, and Cambridge (England) University Hospitals offered WGS to patients with leukemia or solid tumors, respectively. The authors examined 282 tumors from 281 children. The median turnaround time was 18 days for solid tumors and 19 days for hematological malignancies. The tumors examined included 75 distinct entities representing the broad spectrum of pediatric oncological practice. Standard-of-care molecular testing was also performed for all patients as clinically indicated and included tumor and germline testing with copy number arrays; FISH; targeted DNA sequencing; targeted RNA sequencing for fusion detection; and immunohistochemistry or karyotyping, depending on the clinical situation, or both. WGS reproduced findings from the standard-of-care assays and provided additional clinical benefit in 80 instances across 69 of the 282 cases. In addition, WGS led to changes in managing 20 patients. In some cases, WGS identified alterations in genes associated with cancer predisposition that would not normally have been tested. For example, a pathogenic germline PALB2 alteration was identified in a girl with thoracic neuroblastoma. The patient had undergone standard-of-care germline testing, but PALB2 was not interrogated since it is not known to be associated with neuroblastoma. Based on the more recent finding, the patient’s radiotherapy field was adjusted to avoid exposure of breast buds. In other situations, WGS identified novel and disease-defining oncogenic fusions. One infant had a high-grade brain tumor that eluded definitive diagnosis even after standard-of-care molecular testing that included methylation profiling. WGS identified an ATXN1–NUTM2D fusion not previously described in children. The authors concluded that this study demonstrates the clinical utility of WGS in routine pediatric oncology practice. WGS was able to reproduce findings from many standard-of-care molecular assays and provide additional findings in numerous cases. As WGS becomes more efficient and its cost decreases, it may become the mainstay of routine molecular testing.
Hodder A, Leiter SM, Kennedy J, et al. Benefits for children with suspected cancer from routine whole-genome sequencing. Nat Med. doi:10.1038/s41591-024-03056-w
Correspondence: Dr. Matthew J. Murray at mjm16@cam.ac.uk or Dr. Catherine E. Hook at lizhook@nhs.net
Use of whole genome sequencing in diagnosing rare genetic diseases
Large gene panels and exome sequencing are routinely performed in clinical practice to identify the pathogenic variants that cause inherited diseases. In many cases, these assays can identify the causal variants and provide a diagnosis. However, clinical exome sequencing, which examines the protein-coding region of every gene, only interrogates two percent of the genome, so some causal variants may elude detection. Genome sequencing, on the other hand, offers a broader scope. Theoretical advantages of genome sequencing include its ability to detect structural variants, better interrogate repeat expansions, and identify deep intronic events. Furthermore, genome sequencing allows for greater uniformity of sequence coverage since there is no need for an exon capture step in library preparation. A downside to genome sequencing is its higher analytical burden due to the many variants identified that may or may not have clinical relevance. The authors conducted a study in which they performed genome sequencing on 744 families with suspected genetic disease that had previously had a negative diagnostic evaluation. In 29 percent of the families (218 of 744), definite or probable molecular diagnoses were identified by genome sequencing. In 72 percent of those cases, causal variants were identified in previously known disease-associated genes, and in 27.5 percent, the causal variants were in novel disease-associated genes. In 28 percent of the cases, it was determined that genome sequencing was necessary to identify the causal variant. Causal variants that required genome sequencing were rare structural variants (n = 21), repeat expansions (n = 6), or deep intronic variants (n = 15), or they were within regions where depth of coverage improved due to untargeted analysis (n = 19). In 63.5 percent of cases in which genome sequencing identified the causal variant but clinical exome sequencing was negative, the causal variant could be found in the exome sequencing data upon review. The authors suggested that many of these causal variants potentially could be identified by including new disease-associated genes, reinterpreting variants, and incorporating additional methods for analyzing copy-number and mitochondrial DNA variants. However, even under ideal circumstances and with thorough analysis, exome sequencing still would not be able to identify the causal variants in approximately eight percent of patients in this cohort. Based on this finding and because the accessibility of genome sequencing is increasing, this study supports the use of genome sequencing in diagnosing genetic disease, particularly in patients for whom a more targeted approach based on syndromic phenotype has been unsuccessful.
Wojcik MH, Lemire G, Berger E, et al. Genome sequencing for diagnosing rare diseases. N Engl J Med. 2024;390(21):1985–1997.
Correspondence: Dr. Monica Wojcik at monica.wojcik@childrens.harvard.edu or Dr. Anne O’Donnell-Luria at odonnell@broadinstitute.org