Advances in the recognition and management of hereditary cancer

Awareness and utilization of genetic testing for hereditary cancers in cancer survivors: a cross-sectional 2021 HINTS-SEER study

PURPOSE

We aimed to identify factors associated with genetic testing awareness and use among a large sample of US cancer survivors participating in NCI's Health Information National Trends Survey of cancer survivors identified through the Surveillance, Epidemiology, and End Results program, a unique pilot study expanding the number of cancer survivors typically captured by HINTS.

METHODS

We analyzed 2021 HINTS-SEER data to determine sociodemographic factors associated with awareness and utilization of germline genetic testing using survey-weight-adjusted multivariable logistic regression.

RESULTS

Of 1232 survivors (any site), the majority had breast (23%) or prostate (23%) cancer. Among the overall study population, 77% were aware of and 24% utilized genetic testing. Females and those with a college education, income over $100,000, or family history of cancer had greater odds of awareness compared to males, those with less than college education, income under $20,000, or no family history, respectively. Among prostate cancer survivors, those ≥ 65 years in age had lower odds of awareness. Females and the privately insured had greater odds of utilization compared to males and publicly insured, respectively. Those ≥ 65 years or retired had lower odds of utilization compared to < 65 years and being employed, respectively.

CONCLUSION

We identified sociodemographic factors associated with awareness and utilization of germline genetic testing among cancer survivors. Findings warrant further investigation to understand mechanisms underlying disparities in awareness and use of genetic testing.

IMPLICATIONS FOR CANCER SURVIVORS

This study highlights cancer survivor populations that may require additional support around awareness of and use of germline genetic testing.

Genetic and clinical characteristics of genetic tumor syndromes in the central nervous system cancers: Implications for clinical practice

Recognizing individuals with Genetic tumor syndromes (GTS) in the primary central nervous system (CNS) tumors is crucial for optimizing proper genetic counseling and improving therapeutics and clinical care. We retrospectively analyzed the GTS in a Chinese CNS tumor cohort and examined the molecular characteristics and their clinical significance for diagnostic and therapeutic purposes. Our study identified 34 categories of GTS in 258 patients with CNS tumors. The gene with the highest germline pathogenic or likely pathogenic mutation frequency was TP53, followed by MSH2, NF1, and BRCA2. The top five GTS in CNS tumors showed high genetic heterogeneity GTS analysis reclassifies CNS tumors as "NEC." 53.88% of patients diagnosed with GTS harbor potential precision oncology therapy target mutations. The results of our study deepen our understanding of CNS tumors, provide a reference direction for the future design of clinical trials, and further expect to improve disease entire process management in CNS tumors.

Disparate Rates of Germline Variants in Cancer Predisposition Genes in African American/Black Compared With Non-Hispanic White Individuals Between 2015 and 2022

PURPOSE

African American/Black (AA/B) individuals are under-represented in genomic databases and thus less likely to receive definitive information from germline genetic testing (GGT) than non-Hispanic White (NHW) individuals. With nearly 500,000 AA/B and NHW individuals having undergone multigene panel testing (MGPT) for hereditary cancer risk at a single commercial laboratory, to our knowledge, we present the largest study to date investigating cancer GGT results in AA/B and NHW individuals.

METHODS

MGPT results from a retrospective cohort of AA/B (n = 48,684) and NHW (n = 444,831) patients were evaluated. Frequencies of pathogenic germline variants (PGVs) and variants of uncertain significance (VUS) were compared between AA/B and NHW individuals. Changes in frequency of VUS over time were determined. Pearson's chi-squared test was used to compare categorical variables among groups. All significance tests were two-tailed, and P < .05 was considered statistically significant.

RESULTS

Between 2015 and 2022, rates of VUS decreased 2.3-fold in AA/B and 1.8-fold in NHW individuals; however, frequencies of VUS and PGV remained significantly higher (46% v 32%; P < .0001) and lower (9% v 13%; P < .0001) in AA/B compared with NHW individuals. Rates of VUS in ATM, BRCA1, BRCA2, PALB2, and PMS2 were significantly higher in AA/B compared with NHW individuals, whereas rates of PGV in BRCA1, BRCA2, and PALB2 were higher in AA/B compared with NHW individuals (P < .001).

CONCLUSION

Despite reductions in VUS frequencies over time, disparities in definitive GGT results persist. Increasing inclusion of AA/B populations in both testing and research will further increase knowledge of genetic variants across these racial groups.

Using Portuguese BRCA pathogenic variation as a model to study the impact of human admixture on human health

BACKGROUND

Admixture occurs between different ethnic human populations. The global colonization in recent centuries by Europeans led to the most significant admixture in human history. While admixture may enhance genetic diversity for better fitness, it may also impact on human health by transmitting genetic variants for disease susceptibility in the admixture population. The admixture by Portuguese global exploration initiated in the 15th century has reached over 20 million of Portuguese-heritage population worldwide. It provides a valuable model to study the impact of admixture on human health. BRCA1 and BRCA2 (BRCA) are two of the important tumor suppressor genes. The pathogenic variation (PV) in BRCA is well determined to cause high risk of hereditary breast and ovarian cancer. Tracing the distribution of Portuguese BRCA PV in Portuguese-heritage population will help to understand the impact of admixture on cancer susceptibility in modern humans. In this study, we analyzed the distribution of the Portuguese-originated BRCA variation in Brazilian population, which has high degree Portuguese-heritage.

METHODS

By comprehensive data mining, standardization and annotation, we generated a Portuguese-derived BRCA variation dataset and a Brazilian-derived BRCA variation dataset. We compared the two BRCA variation datasets to identify the BRCA variants shared between the two populations.

RESULTS

The Portuguese-derived BRCA variation dataset consists of 220 BRCA variants including 78 PVs from 11,482 Portuguese cancer patients, 93 (42.2%) in BRCA1 and 127 (57.7%) in BRCA2. Of the 556 Portuguese BRCA PV carriers carrying the 78 PVs, 331 (59.5%) carried the three Portuguese-BRCA founder PVs of BRCA1 c.2037delinsCC, BRCA1 c.3331_3334del and BRCA2 c.156_157insAlu. The Brazilian-derived BRCA variation dataset consists of 255 BRCA PVs from 7,711 cancer patients, 136 (53.3%) in BRCA1 and 119 (46.6%) in BRCA2. We developed an open database named dbBRCA-Portuguese ( https://genemutation.fhs.um.edu.mo/dbbrca-portuguese/ ) and an open database named dbBRCA-Brazilian ( https://genemutation.fhs.um.edu.mo/dbbrca-brazilian ) to host the BRCA variation data from Portuguese and Brazilian populations. We compared the BRCA PV datasets between Portuguese and Brazilian populations, and identified 29 Portuguese-specific BRCA PVs shared between Portuguese and Brazilian populations, 14 in BRCA1 including the Portuguese founder BRCA1 c.3331_3334del and BRCA1 c.2037delinsCC, and 15 in BRCA2 including the Portuguese founder BRCA2 c.156_157insAlu. Searching the 78 Portuguese BRCA PVs in over 5,000 ancient human genomes identified evolution origin for only 8 PVs in Europeans dated between 37,470 and 3,818 years before present, confirming the Portuguese-specificity of Portuguese BRCA PVs; comparing the 78 Portuguese BRCA PVs Portuguese, 255 Brazilian BRCA PVs, and 134 African BRCA PVs showed little overlapping, ruling out the possibility that the BRCA PVs shared between Portuguese and Brazilian may also be contributed by African.

CONCLUSION

Our study provides evidence that the admixture in recent human history contributed to cancer susceptibility in modern humans.

A global perspective on the ethnic-specific BRCA variation and its implication in clinical application

Pathogenic BRCA1 and BRCA2 (BRCA) variation is the genetic predisposition for high cancer risk affecting mostly breast and ovarian. BRCA variation information is widely used in clinical diagnosis, treatment, and prevention of BRCA-related cancer. The positive selection imposed on human BRCA leads to highly ethnic-specific BRCA variation to adapt different living environment on earth. Most of the human BRCA variants identified so far were from the European descendant populations and used as the standard reference for global human populations, whereas BRCA variation in other ethnic populations remains poorly characterized. This review addresses the origin of ethnic-specific BRCA variation, the importance of ethnic-specific BRCA variation in clinical application, the limitation of current BRCA variation data, and potential solutions to fill the gap.

Challenges and solutions to the study of rare childhood tumors

PURPOSE OF REVIEW

The majority of progress made in pediatric oncology over the past 50 years has been achieved in the most common cancers. Rare pediatric cancers, which collectively comprise more than 10% of all pediatric cancers, pose multiple challenges to researchers and clinicians, all which stem from the infrequency of these cancers. There has been a tremendous increase in focus on rare pediatric cancers by international consortia and registries, disease-specific clinics, and divisions of academic children's hospitals in the last 10 years. This focus, along with the progress made in cancer genomics, has changed the landscape for the study and treatment of rare pediatric cancers. This review focuses on the past, present, and future of the study and treatment of rare pediatric cancers.

RECENT FINDINGS

Cancer genomics is changing the way some cancers are being diagnosed, categorized, and treated. Rare pediatric cancers potentially stand to greatly benefit from advances in precision diagnosis and treatment.

SUMMARY

The challenges of studying rare pediatric cancers are well known. By utilizing similar techniques that allowed for progress in the common pediatric malignancies, namely collaboration, increased focus, greater funding, and utilization of cancer genomics, progress in the study and treatment of rare pediatric cancers is promising.

Germline variation in BRCA1/2 is highly ethnic-specific: Evidence from over 30,000 Chinese hereditary breast and ovarian cancer patients

BRCA1 and BRCA2 play essential roles in maintaining the genome stability. Pathogenic germline mutations in these two genes disrupt their function, lead to genome instability and increase the risk of developing breast and ovarian cancers. BRCA mutations have been extensively screened in Caucasian populations, and the resulting information are used globally as the standard reference in clinical diagnosis, treatment and prevention of BRCA-related cancers. Recent studies suggest that BRCA mutations can be ethnic-specific, raising the question whether a Caucasian-based BRCA mutation information can be used as a universal standard worldwide, or whether an ethnicity-based BRCA mutation information system need to be developed for the corresponding ethnic populations. In this study, we used Chinese population as a model to test ethnicity-specific BRCA mutations considering that China has one of the latest numbers of breast cancer patients therefore BRCA mutation carriers. Through comprehensive data mining, standardization and annotation, we collected 1,088 distinct BRCA variants derived from over 30,000 Chinese individuals, one of the largest BRCA data set from a non-Caucasian population covering nearly all known BRCA variants in the Chinese population (https://dbBRCA-Chinese.fhs.umac.mo). Using this data, we performed multi-layered analyses to determine the similarities and differences of BRCA variation between Chinese and non-Chinese ethnic populations. The results show the substantial differences of BRCA data between Chinese and non-Chinese ethnicities. Our study indicates that the current Caucasian population-based BRCA data is not adequate to represent the BRCA status in non-Caucasian populations. Therefore, ethnic-based BRCA standards need to be established to serve for the non-Caucasian populations.

Validation of CZECANCA (CZEch CAncer paNel for Clinical Application) for targeted NGS-based analysis of hereditary cancer syndromes

Background

Carriers of mutations in hereditary cancer predisposition genes represent a small but clinically important subgroup of oncology patients. The identification of causal germline mutations determines follow-up management, treatment options and genetic counselling in patients’ families. Targeted next-generation sequencing-based analyses using cancer-specific panels in high-risk individuals have been rapidly adopted by diagnostic laboratories. While the use of diagnosis-specific panels is straightforward in typical cases, individuals with unusual phenotypes from families with overlapping criteria require multiple panel testing. Moreover, narrow gene panels are limited by our currently incomplete knowledge about possible genetic dispositions.

Methods

We have designed a multi-gene panel called CZECANCA (CZEch CAncer paNel for Clinical Application) for a sequencing analysis of 219 cancer-susceptibility and candidate predisposition genes associated with frequent hereditary cancers.

Results

The bioanalytical and bioinformatics pipeline was validated on a set of internal and commercially available DNA controls showing high coverage uniformity, sensitivity, specificity and accuracy. The panel demonstrates a reliable detection of both single nucleotide and copy number variants. Inter-laboratory, intra- and inter-run replicates confirmed the robustness of our approach.

Conclusion

The objective of CZECANCA is a nationwide consolidation of cancer-predisposition genetic testing across various clinical indications with savings in costs, human labor and turnaround time. Moreover, the unified diagnostics will enable the integration and analysis of genotypes with associated phenotypes in a national database improving the clinical interpretation of variants.

Inference of Germline Mutational Status and Evaluation of Loss of Heterozygosity in High-Depth, Tumor-Only Sequencing Data

PURPOSE

Inherited germline defects are implicated in up to 10% of human tumors, with particularly well-known roles in breast and ovarian cancers that harbor BRCA1/2-mutated genes. There is also increasing evidence for the role of germline alterations in other malignancies such as colon and pancreatic cancers. Mutations in familial cancer genes can be detected by high throughput sequencing (HTS), when applied to formalin-fixed paraffin-embedded (FFPE) tumor specimens. However, due to often lack of patient-matched control normal DNA and/or low tumor purity, there is limited ability to determine the genomic status of these alterations (germline versus somatic) and to assess the presence of loss of heterozygosity (LOH). These analyses, especially when applied to genes such as BRCA1/2, can have significant clinical implications for patient care.

METHODS

LOHGIC (LOH-Germline Inference Calculator) is a statistical model selection method to determine somatic-versus-germline status and predict LOH for mutations identified via clinical grade, high-depth, hybrid-capture tumor-only sequencing. LOHGIC incorporates statistical uncertainties inherent to HTS as well as specimen biases in tumor purity estimates, which we use to assess BRCA1/2 mutations in 1,636 specimens sequenced at Rutgers Cancer Institute of New Jersey.

RESULTS

Evaluation of LOHGIC with available germline sequencing from BRCA1/2 testing, demonstrates 93% accuracy, 100% precision, and 96% recall. This analysis highlights a differential tumor spectrum associated with BRCA1/2 mutations.

CONCLUSION

LOHGIC can assess LOH status for both germline and somatic mutations. It also can be applied to any gene with candidate, inherited mutations. This approach demonstrates the clinical utility of targeted sequencing in both identifying patients with potential germline alterations in tumor suppressor genes as well as estimating LOH occurrence in cancer cells, which may confer therapeutic relevance.