Next generation sequencing in cancer research and clinical application

Shyr, Derek; Liu, Qi

doi:10.1186/1480-9222-15-4

Cited by 108 publications

(77 citation statements)

References 91 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Using the similar methodology, we initiated spheroid cells from MDA-MB-231 breast cancer cell lines, which is one of the commonly used TNBC cell line (Chavez, Garimella & Lipkowitz, 2010). Recent advancement in NGS and bioinformatics analysis has provided the opportunity to explore the associated miRNA profiling in the spheroid cell models as a guide for future identification of potential miRNAs markers in breast CSCs studies (Shyr & Liu, 2013). …”

Section: Discussionmentioning

confidence: 99%

Phenotypic and microRNA transcriptomic profiling of the MDA-MB-231 spheroid-enriched CSCs with comparison of MCF-7 microRNA profiling dataset

Boo

Ali

et al. 2017

PeerJ

View full text Add to dashboard Cite

Breast cancer spheroids have been widely used as in vitro models of cancer stem cells (CSCs), yet little is known about their phenotypic characteristics and microRNAs (miRNAs) expression profiles. The objectives of this research were to evaluate the phenotypic characteristics of MDA-MB-231 spheroid-enriched cells for their CSCs properties and also to determine their miRNAs expression profile. Similar to our previously published MCF-7 spheroid, MDA-MB-231 spheroid also showed typical CSCs characteristics namely self-renewability, expression of putative CSCs-related surface markers and enhancement of drug resistance. From the miRNA profile, miR-15b, miR-34a, miR-148a, miR-628 and miR-196b were shown to be involved in CSCs-associated signalling pathways in both models of spheroids, which highlights the involvement of these miRNAs in maintaining the CSCs features. In addition, unique clusters of miRNAs namely miR-205, miR-181a and miR-204 were found in basal-like spheroid whereas miR-125, miR-760, miR-30c and miR-136 were identified in luminal-like spheroid. Our results highlight the roles of miRNAs as well as novel perspectives of the relevant pathways underlying spheroid-enriched CSCs in breast cancer.

show abstract

Section: Discussionmentioning

confidence: 99%

Phenotypic and microRNA transcriptomic profiling of the MDA-MB-231 spheroid-enriched CSCs with comparison of MCF-7 microRNA profiling dataset

Boo

Ali

et al. 2017

PeerJ

View full text Add to dashboard Cite

show abstract

“…This analysis implicates significant computational costs and needs a particular expertise. Although distinct bioinformatics tools have been developed in order to analyze and interpret the increasing amount of sequencing data, sensitivity and efficiency to accurately map noisy reads depends of several factors, such as the choice of single or pair-end reads, the use of long or short reads and the sequencing depth [24]. In this context, the setup of a reliable NGS platform takes a considerable period of time and may represent high costs.…”

Section: Discussionmentioning

confidence: 99%

Whole-Exome Sequencing Enables Rapid Determination of Xeroderma Pigmentosum Molecular Etiology

et al. 2013

View full text Add to dashboard Cite

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by extreme sensitivity to actinic pigmentation changes in the skin and increased incidence of skin cancer. In some cases, patients are affected by neurological alterations. XP is caused by mutations in 8 distinct genes (XPA through XPG and XPV). The XP-V (variant) subtype of the disease results from mutations in a gene (XPV, also named POLH) which encodes for Polη, a member of the Y-DNA polymerase family. Although the presence and severity of skin and neurological dysfunctions differ between XP subtypes, there are overlapping clinical features among subtypes such that the sub-type cannot be deduced from the clinical features.In this study, in order to overcome this drawback, we undertook whole-exome sequencing in two XP sibs and their father. We identified a novel homozygous nonsense mutation (c.897T>G, p.Y299X) in POLH which causes the disease. Our results demonstrate that next generation sequencing is a powerful approach to rapid determination of XP genetic etiology.

show abstract

“…Moreover, NGS technology allows for the identification of base substitution, insertion-deletion, copy number variance, and structural alteration with good sensitivity in cancer [9]. Some studies using NGS have been carried out, obtaining relevant information in breast cancer, lung cancer, ovarian cancer, colorectal cancer, and melanoma [10]. It is important to mention that there are available various NGS techniques that could be applied in cancer, specifically in prostate cancer.…”

Section: Genomic Landscape In Prostate Cancermentioning

confidence: 99%

Genotyping the High Altitude Mestizo Ecuadorian Population Affected with Prostate Cancer

López‐Cortés

Cabrera-Andrade

Salazar-Ruales

et al. 2017

BioMed Research International

View full text Add to dashboard Cite

Prostate cancer (PC) is the second most commonly diagnosed type of cancer in males with 1,114,072 new cases in 2015. The MTHFR enzyme acts in the folate metabolism, which is essential in methylation and synthesis of nucleic acids. MTHFR C677T alters homocysteine levels and folate assimilation associated with DNA damage. Androgens play essential roles in prostate growth. The SRD5A2 enzyme metabolizes testosterone and the V89L polymorphism reduces in vivo SRD5A2 activity. The androgen receptor gene codes for a three-domain protein that contains two polymorphic trinucleotide repeats (CAG, GGC). Therefore, it is essential to know how PC risk is associated with clinical features and polymorphisms in high altitude Ecuadorian mestizo populations. We analyzed 480 healthy and 326 affected men from our three retrospective case-control studies. We found significant association between MTHFR C/T (odds ratio [OR] = 2.2; P = 0.009), MTHFR C/T+T/T (OR = 2.22; P = 0.009), and PC. The SRD5A2 A49T substitution was associated with higher pTNM stage (OR = 2.88; P = 0.039) and elevated Gleason grade (OR = 3.15; P = 0.004). Additionally, patients with ≤21 CAG repeats have an increased risk of developing PC (OR = 2.99; P < 0.001). In conclusion, genotype polymorphism studies are important to characterize genetic variations in high altitude mestizo populations.

show abstract

Next generation sequencing in cancer research and clinical application

Cited by 108 publications

References 91 publications

Phenotypic and microRNA transcriptomic profiling of the MDA-MB-231 spheroid-enriched CSCs with comparison of MCF-7 microRNA profiling dataset

Phenotypic and microRNA transcriptomic profiling of the MDA-MB-231 spheroid-enriched CSCs with comparison of MCF-7 microRNA profiling dataset

Whole-Exome Sequencing Enables Rapid Determination of Xeroderma Pigmentosum Molecular Etiology

Genotyping the High Altitude Mestizo Ecuadorian Population Affected with Prostate Cancer

Contact Info

Product

Resources

About