Bio-informatics Report: Single-cell RNA-Seq in Breast Cancer Analysis

This bioinformatics report explores the application of single-cell RNA sequencing (RNA-Seq) in breast cancer analysis. It begins by contrasting the strengths and weaknesses of microarray technology and RNA-Seq, emphasizing the computational costs associated with the latter. The report discusses a research question focused on how single-cell RNA-Sequencing techniques help in the proper characterization of the breast cancer isolate of different sub-groups of patients, aiming to compare heterogeneity between breast cancer subtypes, detect subtype-specific gene expression at single-cell resolution, and identify specific markers. The methodology involves patient selection, single-cell isolation using microfluidics chips, RNA sequencing, and subsequent data analysis. The report highlights the importance of breast cancer profiling due to its high mortality rates and the limitations of current screening methods. It references several studies, including Castillo et al. (2017) and Chung et al. (2017), to support the use of RNA-Seq for accurate tumor biology assessment and the development of effective screening tools.

Running head: BIO-INFORMATICS
Bio-informatics
Name of the Student
Name of the University
Author Note

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Introduction
Micro-array technology is comparatively less powerful and accurate than Next
Generation RNA-Seq. However, the information contained inside the micro-array is truthful
and robust. On the other hand, RNA-Seq entails high computational costs. The research
undertaken by Castillo et al. (2017), proposed a new model to find signature of gene in cell
lines of breast cancer via integration of heterogeneous data from different datasets of breast
cancer generated via micro-array and RNA-Seq technologies. Castillo et al. (2017) is of the
opinion that integration of data from both the sources provides more robust results, which are
of prime statistical importance. The data can be further utilized for new classification of
breast cancer cell lines along with the establishment of new breast cancer screening tool.
However, combination of both the sequencing techniques can be complex at times.
Suggested future work
The work undertaken by Castillo et al. (2017) helped in the elucidation of the best
bio-markers for the breast cancer via the heterogeneous amalgamation of both RNA-Seq
technologies and micro-array techniques. Chung et al. (2017) of the opinion that the proper
characterization of the tumors cell lines in cancer, which are heterogeneous in nature is best
suited via single-cell transcriptom profiling. It not only helps the characterization of the
heterogeneous tumor cells but also help in the classification of the surrounding immune cells
and stromal cells (Chung et al. 2017).
Research question
How single-cell RNA-Sequencing techniques helps in the proper characterization of
the breast cancer isolate of different sub-groups of patients?

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Aims and objectives
1. Comparison of the heterogeneity between different sub-types of breast cancer
2. To detect the sub-type specific gene expression at single cell resolution
3. Formation of specific markers from the outputs obtained through single cell RNA-Seq
4. Utilization of the generated bio-markers in breast cancer screening
Methods to solve this research question
1. Selection of patients with three different types of breast cancer (Luminal A, Luminal B and
triple negative breast cancer)
2. Isolation of single cells via using sub-typing markers. Sub-typing markers will be validated
via pathological examination
3. Isolation of single cells via using microfluids chips
4. Screening of the single cell via RNA sequencing
5. Detection of the breast cancer heterogeneity
6. Sub-type specific expression of gene at single cell resolution
Influence over the society
Importance of breast cancer profiling is very important in the present day scenario.
According to Youlden et al. (2012), breast cancer is the leading cause of women cancer
causing high rate of mortality worldwide. The mammography screening of breast cancer is
confusing and requires a prolong follow up which is something difficult in the developing
countries (Haukka et al. 2011). Moreover, several multi-gene assays have only few genes in
common. This creates a contradiction in proper screening between different subtypes of
breast cancer (Kittaneh, Montero and Glück 2013). Kittaneh, Montero and Glück (2013) is of

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the opinion that molecular modelling via using sequencing techniques will help to develop
assays that can accurately access tumour biology, pathways to determine growth dependence
of the tumour development along with the clinical behaviour.

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References
Castillo, D., Gálvez, J.M., Herrera, L.J., San Román, B., Rojas, F. and Rojas, I., 2017.
Integration of RNA-Seq data with heterogeneous microarray data for breast cancer
profiling. BMC bioinformatics, 18(1), p.506.
Chung, W., Eum, H.H., Lee, H.O., Lee, K.M., Lee, H.B., Kim, K.T., Ryu, H.S., Kim, S., Lee,
J.E., Park, Y.H. and Kan, Z., 2017. Single-cell RNA-seq enables comprehensive tumour and
immune cell profiling in primary breast cancer. Nature communications, 8, p.15081.
Haukka, J., Byrnes, G., Boniol, M. and Autier, P., 2011. Trends in breast cancer mortality in
Sweden before and after implementation of mammography screening. PLoS One, 6(9),
p.e22422.
Kittaneh, M., Montero, A.J. and Glück, S., 2013. Molecular profiling for breast cancer: a
comprehensive review. Biomarkers in cancer, 5, pp.BIC-S9455.
Youlden, D.R., Cramb, S.M., Dunn, N.A., Muller, J.M., Pyke, C.M. and Baade, P.D., 2012.
The descriptive epidemiology of female breast cancer: an international comparison of
screening, incidence, survival and mortality. Cancer epidemiology, 36(3), pp.237-248.