Molecular subtyping of breast cancer intrinsic taxonomy with oligonucleotide microarray and NanoString nCounter

Breast cancer intrinsic subtypes have been identified based on the transcription of a predefined gene expression (GE) profiles and algorithm (PAM50). This study compared molecular subtyping with oligonucleotide microarray and NanoString nCounter assay. A total of 109 Taiwanese breast cancers (24 with adjacent normal breast tissues) were assayed with Affymetrix Human Genome U133 plus 2.0 microarrays and 144 were assayed with the NanoString nCounter while 64 patients were assayed for both platforms. Subtyping with the nearest centroid (single sample prediction) was performed, and 16 out of 24 (67%) matched normal breasts were categorized as the normal breast-like subtype. For 64 breast cancers assayed for both platforms, 41 (65%, one unclassified by microarray) were predicted with an identical subtype, resulting in a fair Kappa statistic of 0.60. Taking nCounter subtyping as the gold standard, prediction accuracy was 43% (3/7), 81% (13/16), 25% (5/20), and 100% (20/20) for basal-like, HER2-enriched, luminal A and luminal B subtype predicted from microarray GE profiles. Microarray identified more luminal B cases from luminal A subtype predicted by nCounter. It’s not uncommon to use microarray for breast cancer molecular subtyping for research. Our study showed that fundamental discrepancy existed between distinct GE assays, and cross platform equivalence should be carefully appraised when molecular subtyping was conducted with oligonucleotide microarray.

Simultaneous Detection of Ebola Virus and Pathogens Associated With Hemorrhagic Fever by an Oligonucleotide Microarray

Ebola virus infection causes severe hemorrhagic fever, and its mortality rates varied from 25 to 90% in the previous outbreaks. The highly infectious and lethal nature of this virus highlights the need for reliable and sensitive diagnostic methods to distinguish it from other diseases present with similar clinical symptoms. Based on multiplex polymerase chain reaction (PCR) and oligonucleotide microarray technology, a cost-effective, multipathogen and high-throughput method was developed for simultaneous detection of Ebola virus and other pathogens associated with hemorrhagic fever, including Marburg virus, Lassa fever virus, Junin virus, Machupo virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever virus, malaria parasite, hantavirus, severe fever with thrombocytopenia syndrome virus, dengue virus, yellow fever virus, Chikungunya virus, influenza A virus, and influenza B virus. This assay had an excellent specificity for target pathogens, without overlap signal between the probes. The limit of detection was approximately 103 pathogen copies/μl. A total of 60 positive nucleic acid samples for different pathogens were detected, a concordance of 100% was observed between microarray assay and real-time PCR analysis. Consequently, the described oligonucleotide microarray may be specific and sensitive assay for diagnosis and surveillance of infections caused by Ebola virus and other species of hemorrhagic fever pathogens.

Estimation of the heterozygote carrier frequency of frequent hereditary diseases in the Yakuts using oligonucleotide microarray

Цель: определение частоты гетерозиготного носительства частых мутаций среди здоровых индивидов якутской этнической группы с использованием ДНК-биочипа. При генотипировании 120 образцов были выявлены 5 носителей мутации в гене CUL7, 4 - в гене NBAS, 6 носителей мутации в гене DIA1 и 8 - в гене GBJ2. Полученные данные подтверждают ранее полученные данные и свидетельствуют о высокой частоте носительства мутаций в якутской популяции. The aim of current research is to estimate the heterozygote carrier frequency of often found mutations. After genotyping of 120 samples from healthy individuals of yakut ethnic group 5 carriers of mutation in CUL7, 4 carriers of mutation in NBAS, 6 carriers of mutation in DIA1 and 8 carriers in GBJ2 were revealed. The results confirming once again the data previously described by other authors and indicate a high frequency of mutation carriage in the studied genes in population of yakut origin.