Dataset Information

Short tandem repeat analysis for confirmation of uterine non-gestational choriocarcinoma in a postmenopausal Taiwanese woman.

ABSTRACT:

Rationale

Rare uterine choriocarcinoma can be differentiated gestational from nongestational choriocarcinoma by using short tandem repeats (STRs).

Patient concerns

A 56-year-old Taiwanese woman underwent staging surgery because of suspicion of high-grade endometrial cancer. The pathology-confirmed uterine tumor with syncytiotrophoblasts and decidual change of the endometrium was harvested.

Diagnosis

Uterine nongestational choriocarcinoma.

Interventions

The tumor specimen, the patient's blood, and her husband's blood were drawn for STRs analysis using polymerase chain reaction amplification kit. The genotype of the tumor cells was solely maternal and made the diagnosis of uterine nongestational choriocarcinoma.

Outcome

Adjuvant chemotherapy with etoposide, methotrexate, actinomycin D, cyclophosphamide, vincristine regimen achieved good response in the patient. The patient is now recurrence-free for 12 months.

Lessons

STRs aid precise classification of rare choriocarcinoma. We encourage using the method to analyze suspicious choriocarcinoma.

SUBMITTER: Wu CJ

PROVIDER: S-EPMC5841992 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers.We proposed a new dynamic programming based realignment method named STR-realigner that considers repeat patterns in STR regions as prior knowledge. By allowing the size change of repeat patterns with low penalty in STR regions, accurate realignment is expected. For the performance evaluation, publicly available STR variant calling tools were applied to three types of aligned reads: synthetically generated sequencing reads aligned with BWA-MEM, those realigned with STR-realigner, those realigned with ReviSTER, and those realigned with GATK IndelRealigner. From the comparison of root mean squared errors between estimated and true STR region size, the results for the dataset realigned with STR-realigner are better than those for other cases. For real data analysis, we used a real sequencing dataset from Illumina HiSeq 2000 for a parent-offspring trio. RepeatSeq and lobSTR were applied to the sequence reads for these individuals aligned with BWA-MEM, those realigned with STR-realigner, ReviSTER, and GATK IndelRealigner. STR-realigner shows the best performance in terms of consistency of the size of estimated STR regions in Mendelian inheritance. Root mean squared error values were also calculated from the comparison of these estimated results with STR region sizes obtained from high coverage PacBio sequencing data, and the results from the realigned sequencing data with STR-realigner showed the least (the best) root mean squared error value.The effectiveness of the proposed realignment method for STR regions was verified from the comparison with an existing method on both simulation datasets and real whole genome sequencing dataset.