title: Optimization of a pentaplex panel for MSI analysis without control DNA in a Brazilian population: correlation with ancestry markers.
abstract: Microsatellite instability (MSI) testing has been advocated for all newly diagnosed colorectal cancer patients. One of the most common tests is composed by a pentaplex panel of mononucleotides markers (NR-27, NR-21, NR-24, BAT-25, and BAT-26), which allows the analysis of MSI in tumors without the need of reference DNA. For that, it is fundamental to establish a quasi-monomorphic variation range (QMVR) for each marker. Herein, we aimed to establish the QMVR in a Brazilian healthy population, to evaluate the feasibility of MSI determination of tumors, without the matching normal DNA. Furthermore, we intend to assess their ancestry using specific ancestry-informative markers (AIMs) and correlate with QMVR. The QMVR was assessed in 214 individuals, through a pentaplex PCR followed by fragment analysis. The ancestry analysis was done by 46 AIMs in a single multiplex PCR followed by capillary electrophoresis. Following QMVR establishment, we observed 23 individuals with alleles outside the QMVR. Importantly, none of them exhibited more than one marker outside the range. Therefore, individuals with instability at ≥2 markers would be accurately classified as MSI. The European ancestry proportion was the most frequent (67.5%), followed by the African (19.6%). The comparison of the individuals with alleles within (n=191) and outside (n=23) the QMVR showed statistical difference in the proportions of European and African alleles, confirming the higher polymorphic nature of African ancestry. In conclusion, the present study reports an accurate methodology to assess MSI status without matched-normal DNA and independently of the ethnicity, even in the highly admixed population of Brazil.
authors.affiliation: Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil.
authors.forename: Nathália C
authors.initials: NC
authors.lastname: Campanella
authors.affiliation: Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil.
authors.forename: Gustavo N
authors.initials: GN
authors.lastname: Berardinelli
authors.affiliation: Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil.
authors.forename: Cristovam
authors.initials: C
authors.lastname: Scapulatempo-Neto
authors.affiliation: Oncogenetic Department, Barretos Cancer Hospital, São Paulo, Brazil.
authors.forename: Danilo
authors.initials: D
authors.lastname: Viana
authors.affiliation: Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil.
authors.forename: Edenir I
authors.initials: EI
authors.lastname: Palmero
authors.affiliation: IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.
authors.forename: Rui
authors.initials: R
authors.lastname: Pereira
authors.affiliation: 1] Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil [2] Life and Health Sciences Research Institute, University of Minho, and ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal.
authors.forename: Rui M
authors.initials: RM
authors.lastname: Reis
mesh_terms: D000328:Adult; D014408:Biomarkers, Tumor / Q000235:genetics*; D044383:Black People / Q000235:genetics; D001938:Brazil; D018938:Caco-2 Cells; D015179:Colorectal Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D005260:Female; D005820:Genetic Testing / Q000379:methods* / Q000592:standards; D006801:Humans; D008297:Male; D053842:Microsatellite Instability; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods* / Q000592:standards; D044465:White People / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor