Editors: Donna E. Hansel, MD, PhD, chair of pathology, Oregon Health and Science University, Portland; Richard D. Press, MD, PhD, professor and director of molecular pathology, OHSU; James Solomon, MD, PhD, assistant professor, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York; Sounak Gupta, MBBS, PhD, senior associate consultant, Mayo Clinic, Rochester, Minn.; Fei Yang, MD, assistant professor, Department of Pathology, OHSU; Andrés G. Madrigal, MD, PhD, molecular genetic pathology fellow, Department of Pathology, OHSU; and Erica Reinig, MD, assistant professor and medical director of molecular diagnostics, University of Wisconsin-Madison.
Association analysis of breast cancer risk genes in more than 113,000 women
April 2021—Genetic testing for breast cancer hereditary predisposition genes is used to guide cancer screening strategies, risk-reducing surgery, and therapeutic interventions, in accordance with national guidelines. Genetic testing for breast cancer predisposition typically involved testing patients with a strong family history of cancer for a small number of high-risk genes. However, this paradigm has undergone a shift towards testing larger panels of genes as sequencing technologies have become more affordable. An unintended consequence of such testing is that it has led to the identification of alterations in genes that have either a weak association or no link with cancer risk. The authors conducted a multi-institutional international study to better define risk associated with variants in breast cancer predisposing genes. The study involved sequencing germline DNA from more than 60,000 women with breast cancer and more than 50,000 control subjects using 34 genes commonly included in commercial cancer-susceptibility panels. Most of the specimens were from population-based studies, which contrasted with many prior studies that oversampled women with a family history of breast cancer and may have led to biased cancer risk estimates. This study analyzed two major categories of alterations among the genes of interest: variants associated with truncated proteins, which are presumed to confer loss of function, and missense variants that lead to a change in a single amino acid within a protein that can have variable effects on protein function. When the upper limit of the 95 percent confidence interval of the odds ratio pertaining to cancer risk was less than two, the genes of interest were not considered to confer moderate or high risk in this study. Using these criteria, protein-truncated variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 were associated with a high risk of breast cancer (P<.0001). A more modest risk was associated with BARD1, RAD51C, RAD51D, and TP53 (P<.05). In addition, alterations in genes of interest were correlated with hormone receptor status, as hormone receptors are an important biomarker that guides clinical management. Protein-truncating alterations in ATM and CHEK2 had a stronger association with estrogen receptor (ER)-positive breast cancer. The genes BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D were associated with ER-negative breast cancer. Of the latter group, BARD1, BRCA1, and BRCA2 were associated with triple-negative (ER, progesterone receptor, HER2-negative) breast cancer. Among the missense variants, CHEK2, ATM, TP53, BRCA1, CDH1, and RECQL were associated with increased breast cancer risk. Of note, the risk of breast cancer was significantly influenced by the protein-encoding domains in which missense alterations were identified for certain genes. This included the RING domain and BRCT1 domain for BRCA1 and FAT (FRAP-ATM-TRRAP) domain for ATM, while no such association was identified for genes such as CHEK2. An analysis of germline variants in invasive tumors compared with in situ disease revealed that alterations in BRCA1, BRCA2, and PALB2 were frequently associated with invasive tumors. Among the limitations of this study was the analysis of genes such as TP53, in which germline alterations may not have been reliably distinguished from unrecognized somatic mutations in blood specimens due to age-related clonal hematopoiesis. Deleterious alterations in genes associated with cancer syndromes, such as CDH1, PTEN, and STK11, were very rare, while the evidence of an association between breast cancer and several other genes remained equivocal due to wide statistical confidence intervals pertaining to risk estimates. The authors concluded that as genetic testing for breast cancer predisposition genes becomes more widespread, studies such as this will be helpful to determine which genes should be included on NGS-based test panels to predict breast cancer risk and guide genetic counseling.
Breast Cancer Association Consortium. Breast cancer risk genes—association analysis in more than 113,000 women. N Engl J Med. 2021;384(5):428–439.
Correspondence: Dr. D. F. Easton at dfe20@medschl.cam.ac.uk
Molecular diagnostic yield of exome sequencing in people with cerebral palsy
Cerebral palsy is a nonprogressive neurodevelopmental disorder that characteristically impairs movement and posture. It is frequently accompanied by other impairments, including intellectual disability, epilepsy, and autism spectrum disorder. Its prevalence in the United States is estimated to be 2.6 to 2.9 per 1,000 people. Birth asphyxia accounts for less than 10 percent of cases. For the vast majority, the underlying mechanism is unknown. Because diagnosis is often established between six and 11 months of age, the use of genetic testing to identify pathogenic variants early on has significant clinical implications since it may inform the risk of cerebral palsy for future children born to the same parents. In contrast to many prior studies, which interrogated small cohorts of 50 to 250 patients, the authors conducted a study to determine the diagnostic yield of exome sequencing in a large cohort of subjects with an established diagnosis of cerebral palsy. The study focused on a clinical laboratory referral cohort composed of 1,345 pediatric patients (median age, 8.8 years) and a health care-based cohort composed of 181 adult patients (median age, 41.9 years). The former was studied using clinically validated exome analysis, while the latter was evaluated using a research-based exome sequencing analysis. All variants were evaluated for pathogenicity using standardized American College of Medical Genetics/Association for Molecular Pathology interpretation guidelines. A positive diagnostic result, defined as the presence of a pathogenic or likely pathogenic variant, was identified more frequently in the pediatric clinical laboratory referral cohort (32.7 percent) than in the adult health care-based cohort (10.5 percent). A significant difference between the two cohorts involved sequencing the proband and both parents (referred to as “trios”) for 1,009 (75 percent) patients in the clinical laboratory referral cohort. This increased the number of de novo variants identified to 72 percent. Overall, pathogenic or likely pathogenic variants were identified in 29.5 percent of patients in both cohorts combined. This included the identification of 86 genes of interest, in which variants in the same gene were identified in two or more unrelated patients. The genes of interest included those that have been previously implicated in cerebral palsy or other neurodevelopmental disorders, such as CTNNB1, KIF1A, GNAO1, and TUBA1A. These findings strengthened the association of these genes with their putative causative role in cerebral palsy and expanded the associated spectrum of neurodevelopmental disorders seen in these patients. In addition, some patients had variants in the genes AP4E1, AP4M1, AP4S1, ATL1, and SPAST, which are associated with cerebral palsy and hereditary spastic paraplegia. The latter disorder is characterized by progressive neurodegeneration. Furthermore, some mutations involved genes implicated in disorders such as Pitt-Hopkins (TCF4), Rett (MECP2), and Smith-Magenis (17p11.2 deletion) syndromes, which are considered to be clinically distinct from cerebral palsy. In one case, the underlying alteration (SPR) provided clues pertaining to the primary molecular alteration and potential therapy—sepiapterin reductase deficiency leading to dopamine deficiency, with the ability to correct the dopamine deficiency using levodopa in combination with carbidopa. This study was limited by a heterogeneous combined cohort and variation in exome sequencing capture reagents and analytical pipelines between cohorts. However, the identification of pathogenic and likely pathogenic variants in 10.5 percent of adult patients and 32.7 percent of pediatric patients accounted for a significant increase in diagnostic yield. The greatest benefit of such an approach may be for trios testing to help inform the risk of recurrence of cerebral palsy for future children born to the same parents.
Moreno-De-Luca A, Millan F, Pesacreta DR, et al. Molecular diagnostic yield of exome sequencing in patients with cerebral palsy. JAMA. 2021;325(5):467–475.
Correspondence: Dr. Andrés Moreno-De-Luca at amorenodeluca@geisinger.edu