Saliva is a reliable and practical source of germline DNA for genome-wide studies in chronic lymphocytic leukemia

Silvia Rasi; Alessio Bruscaggin; Andrea Rinaldi; Stefania Cresta; Marco Fangazio; Lorenzo de Paoli; Sara Monti; Ernesto Gargiulo; Ivo Kwee; Robin Foà; Francesco Bertoni; Gianluca Gaidano; Davide Rossi

doi:10.1016/j.leukres.2011.05.024

Saliva is a reliable and practical source of germline DNA for genome-wide studies in chronic lymphocytic leukemia

Silvia Rasi, Alessio Bruscaggin, Andrea Rinaldi, Stefania Cresta, Marco Fangazio, Lorenzo de Paoli, Sara Monti, Ernesto Gargiulo, Ivo Kwee, Robin Foà, Francesco Bertoni, Gianluca Gaidano, Davide Rossi^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Research › peer-review

6 Citations (Scopus)

Abstract

High-throughput genomics requires tumor DNA matched to germline DNA, that cannot be easily obtained in the context of leukemia. Using chronic lymphocytic leukemia as a model, saliva DNA was frequently devoid of tumor DNA also during overt disease, and passed quality controls for SNP-array (77/102, 75.4%) and next generation sequencing (71/102, 69.6%). Compared to saliva, urine provides germline DNA of similar quality but in lower amounts. Saliva DNA was successfully run on SNP 6.0 arrays, and passed quality control call rate thresholds. On these bases, saliva represents a useful source of germline DNA for high-throughput genomic studies of hematologic neoplasia.

Original language	English
Pages (from-to)	1419-1422
Number of pages	4
Journal	Leukemia Research
Volume	35
Issue number	10
DOIs	https://doi.org/10.1016/j.leukres.2011.05.024
Publication status	Published - Oct 2011
Externally published	Yes

Keywords

Chronic lymphocytic leukemia
Germline DNA
Next generation sequencing
SNP array
Saliva

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10.1016/j.leukres.2011.05.024Licence: Unspecified

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@article{4fddb0cbe3684da6b5bc157734003b60,

title = "Saliva is a reliable and practical source of germline DNA for genome-wide studies in chronic lymphocytic leukemia",

abstract = "High-throughput genomics requires tumor DNA matched to germline DNA, that cannot be easily obtained in the context of leukemia. Using chronic lymphocytic leukemia as a model, saliva DNA was frequently devoid of tumor DNA also during overt disease, and passed quality controls for SNP-array (77/102, 75.4%) and next generation sequencing (71/102, 69.6%). Compared to saliva, urine provides germline DNA of similar quality but in lower amounts. Saliva DNA was successfully run on SNP 6.0 arrays, and passed quality control call rate thresholds. On these bases, saliva represents a useful source of germline DNA for high-throughput genomic studies of hematologic neoplasia.",

keywords = "Chronic lymphocytic leukemia, Germline DNA, Next generation sequencing, SNP array, Saliva",

author = "Silvia Rasi and Alessio Bruscaggin and Andrea Rinaldi and Stefania Cresta and Marco Fangazio and {de Paoli}, Lorenzo and Sara Monti and Ernesto Gargiulo and Ivo Kwee and Robin Fo{\`a} and Francesco Bertoni and Gianluca Gaidano and Davide Rossi",

note = "Funding Information: This study was supported by Progetto FIRB-Programma “Futuro in Ricerca” 2008 and PRIN 2008, MIUR, Rome, Italy; AIRC, Special Program Molecular Clinical Oncology, 5 × 1000, No. 10007, Milan, Italy; Progetto Giovani Ricercatori 2008, Ministero della Salute, Rome, Italy; and Novara-Associazione Italiana contro le Leucemie, Linfomi e Mielomi (AIL) Onlus, Novara; Helmut Horten Foundation, San Salvatore Foundation, Fondazione per la Ricerca e la Cura sui Linfomi (Lugano, CH). ",

year = "2011",

month = oct,

doi = "10.1016/j.leukres.2011.05.024",

language = "English",

volume = "35",

pages = "1419--1422",

journal = "Leukemia Research",

issn = "0145-2126",

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T1 - Saliva is a reliable and practical source of germline DNA for genome-wide studies in chronic lymphocytic leukemia

AU - Rasi, Silvia

AU - Bruscaggin, Alessio

AU - Rinaldi, Andrea

AU - Cresta, Stefania

AU - Fangazio, Marco

AU - de Paoli, Lorenzo

AU - Monti, Sara

AU - Gargiulo, Ernesto

AU - Kwee, Ivo

AU - Foà, Robin

AU - Bertoni, Francesco

AU - Gaidano, Gianluca

AU - Rossi, Davide

N1 - Funding Information: This study was supported by Progetto FIRB-Programma “Futuro in Ricerca” 2008 and PRIN 2008, MIUR, Rome, Italy; AIRC, Special Program Molecular Clinical Oncology, 5 × 1000, No. 10007, Milan, Italy; Progetto Giovani Ricercatori 2008, Ministero della Salute, Rome, Italy; and Novara-Associazione Italiana contro le Leucemie, Linfomi e Mielomi (AIL) Onlus, Novara; Helmut Horten Foundation, San Salvatore Foundation, Fondazione per la Ricerca e la Cura sui Linfomi (Lugano, CH).

PY - 2011/10

Y1 - 2011/10

N2 - High-throughput genomics requires tumor DNA matched to germline DNA, that cannot be easily obtained in the context of leukemia. Using chronic lymphocytic leukemia as a model, saliva DNA was frequently devoid of tumor DNA also during overt disease, and passed quality controls for SNP-array (77/102, 75.4%) and next generation sequencing (71/102, 69.6%). Compared to saliva, urine provides germline DNA of similar quality but in lower amounts. Saliva DNA was successfully run on SNP 6.0 arrays, and passed quality control call rate thresholds. On these bases, saliva represents a useful source of germline DNA for high-throughput genomic studies of hematologic neoplasia.

AB - High-throughput genomics requires tumor DNA matched to germline DNA, that cannot be easily obtained in the context of leukemia. Using chronic lymphocytic leukemia as a model, saliva DNA was frequently devoid of tumor DNA also during overt disease, and passed quality controls for SNP-array (77/102, 75.4%) and next generation sequencing (71/102, 69.6%). Compared to saliva, urine provides germline DNA of similar quality but in lower amounts. Saliva DNA was successfully run on SNP 6.0 arrays, and passed quality control call rate thresholds. On these bases, saliva represents a useful source of germline DNA for high-throughput genomic studies of hematologic neoplasia.

KW - Chronic lymphocytic leukemia

KW - Germline DNA

KW - Next generation sequencing

KW - SNP array

KW - Saliva

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DO - 10.1016/j.leukres.2011.05.024

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SN - 0145-2126

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EP - 1422

JO - Leukemia Research

JF - Leukemia Research

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ER -

Saliva is a reliable and practical source of germline DNA for genome-wide studies in chronic lymphocytic leukemia

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