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Digital multiplex ligation-dependent probe amplification for detection of key copy number alterations in T- and B-cell lymphoblastic leukemia

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Abstract
Recurrent and clonal genetic alterations are characteristic of different subtypes of T- and B-cell lymphoblastic leukemia (ALL), and several subtypes are strong independent predictors of clinical outcome. A next-generation sequencing based multiplex ligation-dependent probe amplification variant (digitalMLPA) has been developed enabling simultaneous detection of copy number alterations (CNAs) of up to 1000 target sequences. This novel digitalMLPA assay was designed and optimized to detect CNAs of 56 key target genes and regions in ALL. A set of digital karyotyping probes has been included for the detection of gross ploidy changes, to determine the extent of CNAs, while also serving as reference probes for data normalization. Sixty-seven ALL patient samples (including B- and T-cell ALL), previously characterized for genetic aberrations by standard MLPA, array comparative genomic hybridization, and/or single-nucleotide polymorphism array, were analyzed single blinded using digitalMLPA. The digitalMLPA assay reliably identified whole chromosome losses and gains (including high hyperdiploidy), whole gene deletions or gains, intrachromosomal amplification of chromosome 21, fusion genes, and intragenic deletions, which were confirmed by other methods. Furthermore, subclonal alterations were reliably detected if present in at least 20% to 30% of neoplastic cells. The diagnostic sensitivity of the digitaLMLPA assay was 98.9%, and the specificity was 97.8%. These results merit further consideration of digitalMLPA as a valuable alternative for genetic work-up of newly diagnosed ALL patients.
Keywords
CHRONIC LYMPHOCYTIC-LEUKEMIA, IKZF1 DELETION, REARRANGEMENT, HYBRIDIZATION, ABERRATIONS, PROTOCOL, FUSION

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Chicago
Benard-Slagter, Anne, Ilse Zondervan, Karel de Groot, Farzaneh Ghazavi, Virinder Sarhadi, Pieter Van Vlierberghe, Barbara De Moerloose, et al. 2017. “Digital Multiplex Ligation-dependent Probe Amplification for Detection of Key Copy Number Alterations in T- and B-cell Lymphoblastic Leukemia.” Journal of Molecular Diagnostics 19 (5): 659–672.
APA
Benard-Slagter, A., Zondervan, I., de Groot, K., Ghazavi, F., Sarhadi, V., Van Vlierberghe, P., De Moerloose, B., et al. (2017). Digital multiplex ligation-dependent probe amplification for detection of key copy number alterations in T- and B-cell lymphoblastic leukemia. JOURNAL OF MOLECULAR DIAGNOSTICS, 19(5), 659–672.
Vancouver
1.
Benard-Slagter A, Zondervan I, de Groot K, Ghazavi F, Sarhadi V, Van Vlierberghe P, et al. Digital multiplex ligation-dependent probe amplification for detection of key copy number alterations in T- and B-cell lymphoblastic leukemia. JOURNAL OF MOLECULAR DIAGNOSTICS. 2017;19(5):659–72.
MLA
Benard-Slagter, Anne, Ilse Zondervan, Karel de Groot, et al. “Digital Multiplex Ligation-dependent Probe Amplification for Detection of Key Copy Number Alterations in T- and B-cell Lymphoblastic Leukemia.” JOURNAL OF MOLECULAR DIAGNOSTICS 19.5 (2017): 659–672. Print.
@article{8535092,
  abstract     = {Recurrent and clonal genetic alterations are characteristic of different subtypes of T- and B-cell lymphoblastic leukemia (ALL), and several subtypes are strong independent predictors of clinical outcome. A next-generation sequencing based multiplex ligation-dependent probe amplification variant (digitalMLPA) has been developed enabling simultaneous detection of copy number alterations (CNAs) of up to 1000 target sequences. This novel digitalMLPA assay was designed and optimized to detect CNAs of 56 key target genes and regions in ALL. A set of digital karyotyping probes has been included for the detection of gross ploidy changes, to determine the extent of CNAs, while also serving as reference probes for data normalization. Sixty-seven ALL patient samples (including B- and T-cell ALL), previously characterized for genetic aberrations by standard MLPA, array comparative genomic hybridization, and/or single-nucleotide polymorphism array, were analyzed single blinded using digitalMLPA. The digitalMLPA assay reliably identified whole chromosome losses and gains (including high hyperdiploidy), whole gene deletions or gains, intrachromosomal amplification of chromosome 21, fusion genes, and intragenic deletions, which were confirmed by other methods. Furthermore, subclonal alterations were reliably detected if present in at least 20\% to 30\% of neoplastic cells. The diagnostic sensitivity of the digitaLMLPA assay was 98.9\%, and the specificity was 97.8\%. These results merit further consideration of digitalMLPA as a valuable alternative for genetic work-up of newly diagnosed ALL patients.},
  author       = {Benard-Slagter, Anne and Zondervan, Ilse and de Groot, Karel and Ghazavi, Farzaneh and Sarhadi, Virinder and Van Vlierberghe, Pieter and De Moerloose, Barbara and Schwab, Claire and Vettenranta, Kim and Harrison, Christine J and Knuutila, Sakari and Schouten, Jan and Lammens, Tim and Savola, Suvi},
  issn         = {1525-1578},
  journal      = {JOURNAL OF MOLECULAR DIAGNOSTICS},
  keyword      = {CHRONIC LYMPHOCYTIC-LEUKEMIA,IKZF1 DELETION,REARRANGEMENT,HYBRIDIZATION,ABERRATIONS,PROTOCOL,FUSION},
  language     = {eng},
  number       = {5},
  pages        = {659--672},
  title        = {Digital multiplex ligation-dependent probe amplification for detection of key copy number alterations in T- and B-cell lymphoblastic leukemia},
  url          = {http://dx.doi.org/10.1016/j.jmoldx.2017.05.004},
  volume       = {19},
  year         = {2017},
}

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