**4.4. Reproductive health**

transcriptome assembly and annotation for the spice black pepper. Black pepper is one of the most widely used fruit for adding flavor to food as well for its medicinal properties. The authors were able to identify genes that might participate in piperidine, quinolizidine, indolizidine, and lycopodium alkaloid biosynthesis, of which piperidine alkaloids account for pungent taste and medicinal properties of black pepper. Similarly, Shudeesh et al. [135] performed assembly and annotation of field pea, a legume that is cultivated worldwide for human as well as livestock consumption. Studies have also been undertaken to identify transcriptomes of the pathogens that infect economically important plants and the defense mechanisms deployed by the plants. For example, the transcriptome of coffee leaf rust pathogen Hemileia vastatrix was sequenced by Talhinhas et al. [136] to identify genes/ pathways that play a key role in the early stage of the infection, and Yang et al. [137] sequenced the sand pear germplasm with differential resistance to infection by *Alternaria alternata* to

Similar to the value provided by transcriptome profiling of plants, transcriptome profiling of economically important animals contributes toward better understanding of disease resist‐ ance, productivity, breeding, quality of meat, etc., in animals. Ropka-Molik et al. [138] have used the NGS transcriptome profiling approach to identify genes that are differentially expressed between two pig breeds with differences in muscularity that could contribute toward the quality of meat. Gene expression profiles have been generated from different breeds of cows to identify genes that contribute toward milk protein and fat percentage in cow milk [139, 140] and milk yield [141]. Transcriptome profiling has also been used very recently to identify the genes that are differentially expressed in silkworms (*B. mori*) undergoing thermal parthenogenesis [142]. Thermal parthenogenesis is a process that is used in silkworm

Cancer is a complex and heterogeneous genetic disorder that results from either inherited or somatic genetic variations such as single nucleotide variations (SNV), insertions, deletions, copy number variations, dysregulation of gene expression, and epigenetic modifications. As changes in the gene expression pattern play a key role in tumorigenicity [143], metastasis [144], prognosis [145], and relapse [146, 147], gene expression profiling has been used extensively in cancer research and diagnosis. OncotypeDx (http://www.oncotypedx.com/) is a gene-expres‐ sion-based commercially available test that is used for breast cancer, colon cancer, and prostate

Contrary to microarrays and RT-PCR-based approaches used earlier, RNASeq, which can detect coding and noncoding RNA, strand orientation, and genetic variants all in one go, is a very powerful tool in deciphering the complex transcriptome changes usually found in cancer. One of the most comprehensive studies published recently is the transcriptome profiling of 4043 Cancers and 548 Normal Tissue Controls across 12 TCGA Cancer Types [148]. In this study, in addition to identifying tissue specific gene signature, the authors were able to identify

identify genes that contribute toward the resistance.

134 Next Generation Sequencing - Advances, Applications and Challenges

breeding and selection.

cancer diagnosis and prognosis.

**4.3. Cancer**

**4.2. Transcriptome profiling of economically important animals**

With the advancing parental age and a desire to limit the number of pregnancies, many couples opt for assisted reproduction for childbearing. The advanced parental age is a key factor that contributes toward the complications in assisted reproduction, and genomics-based ap‐ proaches are widely used to ensure a high success rate. Gene expression changes in ovarian granulosa cells in women >35 years of age include downregulation of polo-like kinase pathway, which plays an important role in cell cycle arrest of granulosa cells, and the G2/GM checkpoint pathway [151]. Another very recent study also used the RNASeq approach to identify differential gene expression profiles in women with successful pregnancy and a failed pregnancy through assisted reproduction [152]. The authors found that the genes that were differentially expressed played a role in immune response and inflammation, oocyte meiosis, and rhythmic process.

The application of RNASeq in reproductive health is relatively new and as more knowledge is gleaned through this, it might be possible to develop a signature that can be used for predicting the success of assisted reproductive approach.
