Next-Generation Sequencing in Acute Lymphoblastic Leukemia

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2019 Jun 19

PMID 31208040

Citations 42

Authors

Nicoletta Coccaro

Luisa Anelli

Antonella Zagaria

Giorgina Specchia

Francesco Albano

Affiliations

Soon will be listed here.

Abstract

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.

Citing Articles

Clinical characteristics and prognosis of ALL in children with CDKN2A/B gene deletion.

Wang Y, Wu P, Mao X, Jiang N, Huang Y, Zhang L Exp Biol Med (Maywood). 2025; 250:10447.

PMID: 40017529 PMC: 11864878. DOI: 10.3389/ebm.2025.10447.

RanBALL: An Ensemble Random Projection Model for Identifying Subtypes of B-Cell Acute Lymphoblastic Leukemia.

Li L, Xiao H, Wu X, Tang Z, Khoury J, Wang J bioRxiv. 2024; .

PMID: 39386448 PMC: 11463541. DOI: 10.1101/2024.09.24.614777.

Clinical Characteristics and Cytogenetics of Childhood Acute Lymphoblastic Leukemia in a Single Center in Pakistan.

Tabassum N, Muhammad S, Mirza T, Butt Z, Mansoor N Glob Pediatr Health. 2024; 11:2333794X241256863.

PMID: 39070153 PMC: 11283658. DOI: 10.1177/2333794X241256863.

MRD in Philadelphia Chromosome-Positive ALL: Methodologies and Clinical Implications.

Tran V, Salafian K, Michaels K, Jones C, Reed D, Keng M Curr Hematol Malig Rep. 2024; 19(4):186-196.

PMID: 38888822 PMC: 11316691. DOI: 10.1007/s11899-024-00736-9.

Transcriptome Analysis in Mexican Adults with Acute Lymphoblastic Leukemia.

Cruz-Miranda G, Olarte-Carrillo I, Barcenas-Lopez D, Martinez-Tovar A, Ramirez-Bello J, Ramos-Penafiel C Int J Mol Sci. 2024; 25(3).

PMID: 38339034 PMC: 10855968. DOI: 10.3390/ijms25031750.

References

Harrison C, Foroni L . Cytogenetics and molecular genetics of acute lymphoblastic leukemia. Rev Clin Exp Hematol. 2002; 6(2):91-113; discussion 200-2. DOI: 10.1046/j.1468-0734.2002.00069.x. View

Heavey B, Charalambous C, Cobaleda C, Busslinger M . Myeloid lineage switch of Pax5 mutant but not wild-type B cell progenitors by C/EBPalpha and GATA factors. EMBO J. 2003; 22(15):3887-97. PMC: 169053. DOI: 10.1093/emboj/cdg380. View

Xie H, Ye M, Feng R, Graf T . Stepwise reprogramming of B cells into macrophages. Cell. 2004; 117(5):663-76. DOI: 10.1016/s0092-8674(04)00419-2. View

Rivera G, Zhou Y, Hancock M, Gajjar A, Rubnitz J, Ribeiro R . Bone marrow recurrence after initial intensive treatment for childhood acute lymphoblastic leukemia. Cancer. 2004; 103(2):368-76. DOI: 10.1002/cncr.20743. View

Vaskova M, Mejstrikova E, Kalina T, Martinkova P, Omelka M, Trka J . Transfer of genomics information to flow cytometry: expression of CD27 and CD44 discriminates subtypes of acute lymphoblastic leukemia. Leukemia. 2005; 19(5):876-8. DOI: 10.1038/sj.leu.2403706. View

Bruggemann M, Raff T, Flohr T, Gokbuget N, Nakao M, Droese J . Clinical significance of minimal residual disease quantification in adult patients with standard-risk acute lymphoblastic leukemia. Blood. 2005; 107(3):1116-23. DOI: 10.1182/blood-2005-07-2708. View

Graf Einsiedel H, von Stackelberg A, Hartmann R, Fengler R, Schrappe M, Janka-Schaub G . Long-term outcome in children with relapsed ALL by risk-stratified salvage therapy: results of trial acute lymphoblastic leukemia-relapse study of the Berlin-Frankfurt-Münster Group 87. J Clin Oncol. 2005; 23(31):7942-50. DOI: 10.1200/JCO.2005.01.1031. View

Nam C, Rabbitts T . The role of LMO2 in development and in T cell leukemia after chromosomal translocation or retroviral insertion. Mol Ther. 2005; 13(1):15-25. DOI: 10.1016/j.ymthe.2005.09.010. View

Irving J, Minto L, Bailey S, Hall A . Loss of heterozygosity and somatic mutations of the glucocorticoid receptor gene are rarely found at relapse in pediatric acute lymphoblastic leukemia but may occur in a subpopulation early in the disease course. Cancer Res. 2005; 65(21):9712-8. DOI: 10.1158/0008-5472.CAN-05-1227. View

10.

Pui C, Evans W . Treatment of acute lymphoblastic leukemia. N Engl J Med. 2006; 354(2):166-78. DOI: 10.1056/NEJMra052603. View

11.

Van Vlierberghe P, van Grotel M, Beverloo H, Lee C, Helgason T, Buijs-Gladdines J . The cryptic chromosomal deletion del(11)(p12p13) as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemia. Blood. 2006; 108(10):3520-9. DOI: 10.1182/blood-2006-04-019927. View

12.

Raff T, Gokbuget N, Luschen S, Reutzel R, Ritgen M, Irmer S . Molecular relapse in adult standard-risk ALL patients detected by prospective MRD monitoring during and after maintenance treatment: data from the GMALL 06/99 and 07/03 trials. Blood. 2006; 109(3):910-5. DOI: 10.1182/blood-2006-07-037093. View

13.

Fielding A, Richards S, Chopra R, Lazarus H, Litzow M, Buck G . Outcome of 609 adults after relapse of acute lymphoblastic leukemia (ALL); an MRC UKALL12/ECOG 2993 study. Blood. 2006; 109(3):944-50. DOI: 10.1182/blood-2006-05-018192. View

14.

van der Velden V, Cazzaniga G, Schrauder A, Hancock J, Bader P, Panzer-Grumayer E . Analysis of minimal residual disease by Ig/TCR gene rearrangements: guidelines for interpretation of real-time quantitative PCR data. Leukemia. 2007; 21(4):604-11. DOI: 10.1038/sj.leu.2404586. View

15.

Mullighan C, Goorha S, Radtke I, Miller C, Coustan-Smith E, Dalton J . Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature. 2007; 446(7137):758-64. DOI: 10.1038/nature05690. View

16.

Lahortiga I, De Keersmaecker K, Van Vlierberghe P, Graux C, Cauwelier B, Lambert F . Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia. Nat Genet. 2007; 39(5):593-5. DOI: 10.1038/ng2025. View

17.

Kuiper R, Schoenmakers E, van Reijmersdal S, Hehir-Kwa J, Geurts van Kessel A, van Leeuwen F . High-resolution genomic profiling of childhood ALL reveals novel recurrent genetic lesions affecting pathways involved in lymphocyte differentiation and cell cycle progression. Leukemia. 2007; 21(6):1258-66. DOI: 10.1038/sj.leu.2404691. View

18.

Clappier E, Cuccuini W, Kalota A, Crinquette A, Cayuela J, Dik W . The C-MYB locus is involved in chromosomal translocation and genomic duplications in human T-cell acute leukemia (T-ALL), the translocation defining a new T-ALL subtype in very young children. Blood. 2007; 110(4):1251-61. DOI: 10.1182/blood-2006-12-064683. View

19.

Palomero T, Sulis M, Cortina M, Real P, Barnes K, Ciofani M . Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nat Med. 2007; 13(10):1203-10. PMC: 2600418. DOI: 10.1038/nm1636. View

20.

Kawamata N, Ogawa S, Zimmermann M, Kato M, Sanada M, Hemminki K . Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray. Blood. 2007; 111(2):776-84. PMC: 2200831. DOI: 10.1182/blood-2007-05-088310. View