Comparative study of aCGH and Next Generation Sequencing (NGS) for chromosomal microdeletion and microduplication screening.
BACKGROUND
prenatal genetic diagnosis of rare disorders is undergoing in recent years a significant enhancement through the application of methods of massive parallel sequencing. Despite the quantity and quality of the data produced, just few analytical tools and software have been developed in order to identify structural and numerical chromosomal anomalies through NGS, mostly not compatible with benchtop NGS platform and routine clinical diagnosis.


METHODS
we developed technical, bioinformatic, interpretive and validation pipelines for Next Generation Sequencing to identify SNPs, indels, aneuploidies, and CNVs (Copy Number Variations).


RESULTS
we show a new targeted resequencing approach applied to prenatal diagnosis. For sample processing we used an enrichment method for 4,813 genes library preparation; after sequencing our bioinformatic pipelines allowed both SNPs analysis for approximately thirty diseases or diseases family involved in fetus development and numerical chromosomal anomalies screening.


CONCLUSIONS
results obtained are compatible with those obtained through the gold standard technique, aCGH array, moreover allowing identification of genes involved in chromosome deletions or duplications and exclusion of point mutation on allele not affected by chromosome aberrations.
Department of Genetics, Altamedica-Artemisia, Rome, Italy.
Claudio Dello
CD
Russo
Department of Genetics, Altamedica-Artemisia, Rome, Italy.
Gianluca
G
Di Giacomo
Department of Fetal Maternal Medicine, Altamedica-Artemisia, Rome, Italy.
Pietro
P
Cignini
Department of Fetal Maternal Medicine, Altamedica-Artemisia, Rome, Italy.
Francesco
F
Padula
Department of Fetal Maternal Medicine, Altamedica-Artemisia, Rome, Italy.
Lucia
L
Mangiafico
Department of Genetics, Altamedica-Artemisia, Rome, Italy.
Alvaro
A
Mesoraca
Department of Fetal Maternal Medicine, Altamedica-Artemisia, Rome, Italy.
Laura
L
D'Emidio
Softgenetics LLC, State College, Pennsylvania, USA.
Megan R
MR
McCluskey
Diatech Lab Line, Jesi, Italy.
Arianna
A
Paganelli
Department of Fetal Maternal Medicine, Altamedica-Artemisia, Rome, Italy.
Claudio
C
Giorlandino
Copy Number Variation (CNV); next generation sequencing; prenatal diagnosis