Highly sensitive detection of GATA1 mutations in patients with myeloid leukemia associated with Down syndrome by combining Sanger and targeted next generation sequencing

2019 ◽  
Vol 59 (3) ◽  
pp. 160-167 ◽  
Author(s):  
Kiminori Terui ◽  
Tsutomu Toki ◽  
Takashi Taga ◽  
Shotaro Iwamoto ◽  
Takako Miyamura ◽  
...  
Keyword(s):  
Down Syndrome ◽  
Next Generation Sequencing ◽  
Myeloid Leukemia ◽  
Sensitive Detection ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Highly Sensitive ◽  
Highly Sensitive Detection ◽  
Generation Sequencing

Targeted Next-Generation Sequencing of 406 Genes Identified Genetic Defects Underlying Congenital Heart Disease in Down Syndrome Patients

2018 ◽  
Vol 39 (8) ◽  
pp. 1676-1680 ◽  
Author(s):  
Khalid M. Alharbi ◽  
Abdelhadi H. Al-Mazroea ◽  
Atiyeh M. Abdallah ◽  
Yousef Almohammadi ◽  
S. Justin Carlus ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Down Syndrome ◽  
Heart Disease ◽  
Next Generation Sequencing ◽  
Congenital Heart ◽  
Genetic Defects ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

scholarly journals A customized scaffolds approach for the detection and phasing of complex variants by next-generation sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qiandong Zeng ◽  
Natalia T. Leach ◽  
Zhaoqing Zhou ◽  
Hui Zhu ◽  
Jean A. Smith ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Variant Calling ◽  
Causative Mutation ◽  
Next Generation ◽  
Single Nucleotide ◽  
Highly Sensitive ◽  
Highly Sensitive Detection ◽  
Next Generation Sequencing Ngs ◽  
Reference Bias ◽  
Generation Sequencing

Abstract Next-generation sequencing (NGS) is widely used in genetic testing for the highly sensitive detection of single nucleotide changes and small insertions or deletions. However, detection and phasing of structural variants, especially in repetitive or homologous regions, can be problematic due to uneven read coverage or genome reference bias, resulting in false calls. To circumvent this challenge, a computational approach utilizing customized scaffolds as supplementary reference sequences for read alignment was developed, and its effectiveness demonstrated with two CBS gene variants: NM_000071.2:c.833T>C and NM_000071.2:c.[833T>C; 844_845ins68]. Variant c.833T>C is a known causative mutation for homocystinuria, but is not pathogenic when in cis with the insertion, c.844_845ins68, because of alternative splicing. Using simulated reads, the custom scaffolds method resolved all possible combinations with 100% accuracy and, based on > 60,000 clinical specimens, exceeded the performance of current approaches that only align reads to GRCh37/hg19 for the detection of c.833T>C alone or in cis with c.844_845ins68. Furthermore, analysis of two 1000 Genomes Project trios revealed that the c.[833T>C; 844_845ins68] complex variant had previously been undetected in these datasets, likely due to the alignment method used. This approach can be configured for existing workflows to detect other challenging and potentially underrepresented variants, thereby augmenting accurate variant calling in clinical NGS testing.

scholarly journals Targeted next-generation sequencing of circulating cell-free DNA vs bone marrow in patients with acute myeloid leukemia

2020 ◽  
Vol 4 (8) ◽  
pp. 1670-1677
Author(s):  
Nicholas J. Short ◽  
Keyur P. Patel ◽  
Maher Albitar ◽  
Miguel Franquiz ◽  
Rajyalakshmi Luthra ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Acute Myeloid Leukemia ◽  
Next Generation Sequencing ◽  
Myeloid Leukemia ◽  
Next Generation ◽  
Cell Free Dna ◽  
Targeted Next Generation Sequencing ◽  
Free Dna ◽  
Generation Sequencing ◽  
Acute Myeloid

Abstract Circulating cell-free DNA (ccfDNA) allows for noninvasive peripheral blood sampling of cancer-associated mutations and has established clinical utility in several solid tumors. We performed targeted next-generation sequencing of ccfDNA and bone marrow at the time of diagnosis and after achieving remission in 22 patients with acute myeloid leukemia (AML). Among 28 genes sequenced by both platforms, a total of 39 unique somatic mutations were detected. Five mutations (13%) were detected only in ccfDNA, and 15 (38%) were detected only in bone marrow. Among the 19 mutations detected in both sources, the concordance of variant allelic frequency (VAF) assessment by both methods was high (R2 = 0.849). Mutations detected in only 1 source generally had lower VAF than those detected in both sources, suggesting that either method may miss small subclonal populations. In 3 patients, sequencing of ccfDNA detected new or persistent leukemia-associated mutations during remission that appeared to herald overt relapse. Overall, this study demonstrates that sequencing of ccfDNA in patients with AML can identify clinically relevant mutations not detected in the bone marrow and may play a role in the assessment of measurable residual disease. However, mutations were missed by both ccfDNA and bone marrow analyses, particularly when the VAF was <10%, suggesting that ccfDNA and bone marrow may be complementary in the assessment and monitoring of patients with AML.

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