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Newswise BUFFALO, N.Y. The Jewels in our Genes study, led by University at Buffalo researcher Heather Ochs-Balcom, has uncovered previously unknown segments of DNA shared by African American family members who have breast cancer.

The discovery of these regions supports our hypothesis that there are still undiscovered breast cancer genes that may be unique to African Americans, says Ochs-Balcom, PhD, a genetic epidemiologist in the UB Department of Epidemiology and Environmental Health. We can now focus on these specific chromosomes to learn if they house genetic mutations linked to breast cancer.

We also need to determine whether those mutations are found in other racial groups or if they are unique to African Americans. If they are unique, it could explain why young African American women have a higher risk of pre-menopausal breast cancer compared to other groups, she says.

Our study used linkage analysis, a powerful tool that helps to detect the chromosomal location of disease genes by examining genetic markers across the entire human genome. Our family-based gene hunt is similar to the groundbreaking study among women with European ancestry done in the early 1990s that led to the discovery of BRCA1 and BRCA2 gene mutations, which greatly increase susceptibility to breast and ovarian cancer.

African American women can also carry the BRCA mutations, but Ochs-Balcom suspects there may be additional, undiscovered mutations linked to breast cancer in this population.

Family studies like this one have been difficult to conduct in the past, Ochs-Balcom says, in part because its difficult to get multiple family members to commit the time needed to participate. We found here that approaching the recruitment of African Americans by using a multi-pronged approach that included collaboration from our community partnerships greatly facilitated success.

She points out that African American women have a higher incidence of pre-menopausal breast cancer and a higher breast cancer mortality rate than European Americans. They also more likely to develop early-onset cancers that are aggressive and difficult to treat. Some of these may be caused by unknown genetic anomalies that if found, could lead to early screening, detection and treatment.

The study was funded by a grant from the Susan G. Komen for the Cure Foundation and is the subject of two recent papers published by the team in the journal Cancer, Epidemiology, Biomarkers and Prevention and the Journal of Community Genetics.

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Study Links New Genetic Anomalies to Breast Cancer in African American Families

3 hours ago RGEN-induced digenome sequencing to capture off-target sites. (a) Overview of Digenome-seq. Forward and reverse sequence reads are shown in pink and blue, respectively. Red triangles and vertical lines indicate cleavage positions. WT, wild type. (b) Representative IGV images obtained using the HBB-specific RGEN at the on-target site.

The IBS research team (Center for Genome Engineering) has successfully confirmed that CRISPR-Cas9 has accurate on-target effects in human cells, through joint research with the Seoul National University College of Medicine and ToolGen, Inc.

There has been great interest in CRISPR-Cas9 as a tool to develop anticancer cell therapies or to correct genetic defects that cause hereditary in stem and somatic cells. However, since there has been no reliable and sensitive method to measure the accuracy of CRISPR-Cas9 genome-wide, its safety has remained in question. Consequently, it has been difficult to eliminate the possibility that CRISPR-Cas9 may induce mutations in off-target sequences that are similar to on-target sequences. Off-target mutations in tumor suppressor genes, for example, can cause cancer.

The researchers have developed a technique termed Digenome-seq to locate both on-target and off-target sequences that can be mutated by CRISPR-Cas9 via genome sequencing. They digested human genomic DNA using Cas9 nucleases in a test tube, which was then subjected by whole genome sequencing. This in vitro digest yielded a unique pattern at both on-target and off-target sequences that can be computationally identified. Furthermore, by adding guanine nucleotides at the end of sgRNA(single guided RNA) that composes CRISPR-Cas9, they have successfully created this highly-developed programmable nuclease, which has no measurable off-target effects in the human genome.

Jin-Soo Kim, the director of the Center for Genome Engineering at IBS, as well as the professor of the Department of Chemistry at Seoul National University says, "If CRISPR-Cas9 truncates off-target DNA sequences, it might induce unwanted mutations. Since we have succeeded in confirming the accuracy of CRISPR-Cas9, we anticipate that there will be a great progress in the development of gene or cell therapies," emphasizing the significance of this research achievement.

Nature Methods has also highlighted this achievement as one of the "2015 Methods to Watch" in its January issue.

Explore further: Revolutionizing genome engineering: Review on history and future of the CRISPR-Cas9 system published

More information: Daesik Kim, Sangsu Bae, Jeongbin Park, Eunji Kim, Seokjoong Kim, Hye Ryeong Yu, Jinha Hwang, Jong-Il Kim & Jin-Soo Kim.(2015) Nature Methods. DOI: 10.1038/nmeth.3284

Journal reference: Nature Methods

Provided by Institute for Basic Science

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End of CRISPR-CAS9 controversy