Detection of fetal genetic disorders through non-invasive prenatal testing using next-generation sequencing

• Grant number: 13/14996-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: February 01, 2014
• End date: July 31, 2017
• Field of knowledge: Biological Sciences - Genetics - Human and Medical Genetics
• Principal Investigator: Maria Rita dos Santos e Passos Bueno
• Grantee: Carolina Malcher Amorim de Carvalho Silva
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 13/08028-1 - CEGH-CEL - Human Genome and Stem Cell Research Center, AP.CEPID
• Associated scholarship(s): 15/11998-8 - Analysis of cell-free DNA sequencing data in order to infer the fetal fraction of cell-free DNA in maternal plasma, BE.EP.DR

Abstract

The chromosomal abnormalities account for about 6% of cases of congenital anomalies, and the aneuploidies are the most commonly found. Among the autosomal aneuploidies, the most significant are the Down syndrome (Trisomy 21), Edwards (Trisomy 18) and Patau syndromes (Trisomy 13). Currently, the diagnosis of these diseases is performed by karyotype or FISH of fetal genetic material obtained through invasive procedures, which represent various risks, including fetal loss. The discovery of cell-free fetal DNA (cffDNA) in the maternal circulation allowed several studies focusing on prenatal diagnosis by non-invasive detection of cffDNA in the maternal plasma. This is currently done for some traits, such as fetal sex determination and Rh factor, and more recently, detection of aneuploidy. However, the detection of monogenic diseases is still in its initial state. The aim of this work is to develop a noninvasive prenatal detection test of genetic disorders in fetuses using next-generation sequencing. For trisomies, the chromosomes 21 and 18 will be tested, and for monogenic disease, Duchenne muscular dystrophy. In order to do this, probes for detecting both non-polymorphic and polymorphic loci will be used for estimating both trisomy and the fraction of cffDNA. The detection of trisomies will be performed through the sequencing counts of non-polymorphic loci on the chromosomes of interest, whilst for the determination of the fraction of cffDNA present in maternal plasma, informative SNPs for the Brazilian population will be used across autosomes. Regarding the methodology to be used, there are still many questions to be answered, such as what is the minimum amount of probes needed, as well as the feasibility of identification of pathogenic point mutations. Another important issue to address in our population is the cffDNA proportion, which can vary according to ethnicity, gestational age and maternal weight, and which values are fundamental to ensure the efficiency of the noninvasive prenatal screening.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

MALCHER, CAROLINA; YAMAMOTO, GUILHERME L.; BURNHAM, PHILIP; EZQUINA, SUZANA A. M.; LOURENCO, V, NAILA C.; BALKASSMI, SAHILLA; MARCO ANTONIO, DAVID S.; HSIA, GABRIELLA S. P.; GOLLOP, THOMAZ; PAVANELLO, RITA C.; et al. Development of a comprehensive noninvasive prenatal test. GENETICS AND MOLECULAR BIOLOGY, v. 41, n. 3, p. 545-554, JUL-SEP 2018. (15/11998-8, 13/14996-0, 13/08028-1)

MALCHER, CAROLINA; YAMAMOTO, GUILHERME L.; BURNHAM, PHILIP; EZQUINA, SUZANA A. M.; LOURENCO, NAILA C., V; BALKASSMI, SAHILLA; MARCO ANTONIO, DAVID S.; HSIA, GABRIELLA S. P.; GOLLOP, THOMAZ; PAVANELLO, RITA C.; et al. Development of a comprehensive noninvasive prenatal test. GENETICS AND MOLECULAR BIOLOGY, v. 41, n. 3, p. 10-pg., 2018-07-01. (13/08028-1, 15/11998-8, 13/14996-0)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

SILVA, Carolina Malcher Amorim de Carvalho. Noninvasive prenatal test for detection of genetic diseases using next-generation sequencing. 2017. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Biociências (IBIOC/SB) São Paulo.