Complex structural chromosome abnormalities are common in cancer cells. Besides the
well-known mechanism of gradual accumulation of mutations to prefer cell duplication/survival
in cancer cells, complex and massive chromosomal and genomic alterations can also
be generated by a chromoanagenesis event, which is characterized by the simultaneous
occurrence of multiple structural alterations through a single catastrophic cellular
event. Despite improvements in genomics technology, the detection of complex structural
chromosome abnormalities from short-read sequencing still poses challenges. The nanopore
can sequence stretches of DNA of up to hundreds of kilobases in length and clustered
regularly interspaced short palindromic repeats (CRISPR) Cas9 is a novel gene-editing
technique, which can efficiently induce targeted genetic modifications. Here we analyzed
a cancer genome of a patient using the CRISPR Cas9-mediated targeted sequencing on
nanopore. The patient suffered from acute myeloid leukemia resulting from a complex
karyotype: 44,XY,add(1)(p12),t(1;4)(p13;q31.1), add(2)(p13),-3,-5,add(6)(q25),der(7)?hsr(7)(q11.2)?hsr(7)(q?22)t(3;7)(p12;q?31),-16,
der(16)t(16;17)(q12.1;q11.2),-17,add(17)(p13),del(17)(p13),add(20)(q11.2), der(?)t(?;1)(?;p22)[cp18]/46,XY[2].
FISH revealed amplification of chromosome 7 centromere. Illumina genome-wide SNP microarray
revealed 9 gains, 20 losses, as well as three chromoanagenesis regions (3q12.2-q13.31,
3q13.32-q21.3, and 7p12.2-q11.2). CRISPR Cas9 probes for breakpoints of these abnormalities
were designed. Protein nanopores were used to measure DNA sequence directly and in
real time. The long reads from the nanopore not only determined simple structural
abnormalities, but also enabled us to resolve the long-range structure of the complex
chromoanagenesis. In summary, sequencing cancer genome of our patient using CRISPR
Cas9-mediated targeted sequencing on nanopore detected breakpoints of complex structural
chromosome abnormalities, at high sensitivity. We demonstrated the value of this approach
in mapping complex structural chromosome abnormalities for both clinical and research
applications. Characterization of these complex structural chromosome abnormalities
will not only help understand the molecular mechanisms responsible for a process of
chromoanagenesis, but also may identify specific molecular targets and their impact
on therapy and overall survival.
To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:
Subscribe to Cancer GeneticsAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
Article Info
Identification
Copyright
© 2021 Published by Elsevier Inc.