Li Hui Tseng

Clinical Validation of KRAS, BRAF, and EGFR Mutation Detection Using Next-Generation Sequencing

OBJECTIVES To validate next-generation sequencing (NGS) technology for clinical diagnosis and to determine appropriate read depth. METHODS We validated the KRAS, BRAF, and EGFR genes within the Ion AmpliSeq Cancer Hotspot Panel using the Ion Torrent Personal Genome Machine (Life Technologies, Carlsbad, CA). RESULTS We developed a statistical model to determine the read depth needed for a given percent tumor cellularity and number of functional genomes. Bottlenecking can result from too few input genomes. By using 16 formalin-fixed, paraffin-embedded (FFPE) cancer-free specimens and 118 cancer specimens with known mutation status, we validated the six traditional analytic performance characteristics recommended by the Next-Generation Sequencing: Standardization of Clinical Testing Working Group. Baseline noise is consistent with spontaneous and FFPE-induced C:G→T:A deamination mutations. CONCLUSIONS Redundant bioinformatic pipelines are essential, since a single analysis pipeline gave false-negative and false-positive results. NGS is sufficiently robust for the clinical detection of gene mutations, with attention to potential artifacts.

Molecular genetic study of Pompe disease in Chinese patients in Taiwan

Pompe disease is caused by mutations in the acid α‐glucosidase (GAA) gene. Multiple kinds of mutations in the GAA gene have been reported worldwide. In order to elucidate the molecular basis of the disease in Taiwanese patients of Chinese origin, we have recruited 11 unrelated families who had at least one member with Pompe disease for study. We used 16 pairs of oligonucleotide primers to amplify all the coding regions from exon 2 to 20 in the family members. The coding regions were sequenced on both the sense and antisense strands. We identified 7 different mutations in 17 alleles but failed to identify the defects in the other 5 alleles. The most common defect was D645E (Asp645Glu), accounting for 36% (8/22 alleles) of mutations, followed by G615R (Gly615Arg) (3 alleles); 1411del4 (Glu471‐shift) (2 alleles); and one allele each of R600H (Arg600His); ΔN675 (ΔAsn675); 2380delC (Arg794‐shift) and 2815delGT (Val939‐shift). The molecular defects of Pompe disease are highly heterogeneous in Chinese. Characterization of the molecular defects of the disease is useful for a genotype‐phenotype correlation and for genetic counseling and prenatal diagnosis. Hum Mutat 13:380–384, 1999.

Carrier detection and prenatal diagnosis of alpha-thalassemia of Southeast Asian deletion by polymerase chain reaction

SummaryAlpha-thalassemia of Southeast Asian deletion (-- SEA/) is very common in Southeast Asia. Homozygosity of this genotype is the major cause of Hb Barts hydrops fetalis in Taiwan. With polymerase chain reaction using three oligonucleotide primers bridging the common deletion breakpoint, a DNA fragment of 194 basepairs (bp) was amplified in chromosomes with the-- SEA determinant and a DNA fragment of 287 bp was amplified in chromosomes without this deletion. In our pilot study including 8 normal subjects, 20 obligate carriers, and 11 homozygotes of the deletion, all the genotypes were determined and then confirmed by Southern blotting and DNA hybridization with φζ globin gene probe. For prenatal diagnosis, 55 at-risk pregnancies were collected. Chorionic villus sampling was done in 51 cases and early amniocentesis was done in 4 cases. Fourteen cases (25.5%) were diagnosed as normal, 25 (45.5%) as heterozygotes, and 16 (29%) as homozygotes of -- SEA. All of the diagnoses were also confirmed as aforementioned. With polymerase chain reaction, the determination of the -- SEA deletion is straightforward and is much quicker and easier than with conventional Southern blotting and DNA hybridization. In areas with a high prevalence of -- SEA deletion, this method provides a rapid tool for carrier detection and prenatal diagnosis.

Amniocentesis in mothers who are hepatitis B virus carriers does not expose the infant to an increased risk of hepatitis B virus infection

Sixty-seven pairs of mothers with hepatitis B virus (HBV) surface antigen (HBsAg) and their infants were divided into two study groups to determine the effect of amniocentesis on intrauterine HBV infection. In the first study group (35 pairs), the infants HBsAg status in cord blood was studied and the results were compared with those obtained in the cord blood from 65 infants born to HBsAg-positive women who did not have an amniocentesis. In the second study group (32 pairs), the HBV status of the infants was studied at the age of three months to five years and compared with the HBV status of 3,454 infants in the National HBV Prevention Program. In the first study group, one sample (2.9%) was weakly positive for HBsAg; while in the first control group, two (3.1%) were positive. In the second study group, three (10%) infants were positive for HBsAg. The failure rates of immunoprophylaxis in the second study and control groups were similar (9.4% vs 11% for HBsAg carrier mothers; 30% vs 14% for HBe antigen-positive carrier mothers). This suggested that genetic amniocentesis did not increase the risk of intrauterine HBV infection.

SIMULTANEOUS GENOTYPING OF SINGLE NUCLEOTIDE POLYMORPHISMS IN THE IL-1 GENE COMPLEX BY MULTIPLEX POLYMERASE CHAIN REACTION-RESTRICTION FRAGMENT LENGTH POLYMORPHISM

The interleukin-1 (IL-1) gene complex consists of the IL-1alpha, IL-1beta and IL-1 receptor antagonist genes. Single-nucleotide polymorphisms (SNP) in all three genes have been associated with human diseases. In this study, primers containing mismatches at 1-3 nucleotide positions were designed to incorporate a restriction site for endonuclease AlwNI or XcmI in the presence of allele-specific nucleotides at the polymorphic positions. Based on this technique, a simple and robust multiplex polymerase chain reaction/restriction fragment length polymorphism (multiplex PCR/RFLP) assay was developed to determine simultaneously three to four informative SNPs (IL-1beta/+3954, IL-1beta/-511 and IL-1Ra/9261 or IL-1alpha/-889, IL-1beta/-31, IL-1beta/5810 and IL-1Ra/11100 SNPs) in the IL-1 gene complex.

IL10 and IL10 receptor gene variation and outcomes after unrelated and related hematopoietic cell transplantation.

Background. Results of a previous study with human leukocyte antigen (HLA)-identical siblings showed individual and synergistic associations of single nucleotide polymorphisms in the promoter region of the recipient’s IL10 gene and the donor’s IL10 receptor &bgr; (IL-10RB) gene with development of grades III–IV acute graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation. Methods. In this study of 936 patients who had unrelated donors, genotypes of single nucleotide polymorphisms in the IL10 gene and the IL-10RB gene were evaluated as correlates with outcomes after transplantation. Results. We found no statistically significant associations of polymorphisms at positions −3575, −2763, −1082, and −592 of the IL10 gene or codon 238 of the IL10RB gene with severe acute GVHD, extensive chronic GVHD or nonrelapse mortality after hematopoietic cell transplantation. Among HLA-matched unrelated pairs, the patient’s IL10/−592 genotype and donor’s IL10RB/c238 genotype showed trends suggesting individual and combined associations with grades III–IV acute GVHD similar to those observed among patients with HLA-identical sibling donors. Conclusions. Although genetic variation in IL10 pathway affects risk of acute GVHD and non-relapse mortality in HLA-identical sibling transplants, the current results indicate that genetic variation in the IL10 pathway does not significant affect these outcomes in unrelated donor transplants suggesting that the strength of the alloimmune response in the latter exceeds the anti-inflammatory activity of IL10.

Mutational profiling of colorectal cancers with microsatellite instability

Microsatellite instability (MSI) is caused by defective mismatch repair in 15–20% of colorectal cancers (CRCs). Higher mutation loads in tumors with mismatch repair deficiency can predict response to pembrolizumab, an anti-programmed death 1 (PD-1) immune checkpoint inhibitor. We analyzed the mutations in 113 CRCs without MSI (MSS) and 29 CRCs with MSI-High (MSI-H) using the 50-gene AmpliSeq cancer panel. Overall, MSI-H CRCs showed significantly higher mutations than MSS CRCs, including insertion/deletion mutations at repeat regions. MSI-H CRCs showed higher incidences of mutations in the BRAF, PIK3CA, and PTEN genes as well as mutations in the receptor tyrosine kinase families. While the increased mutations in BRAF and PTEN in MSI-H CRCs are well accepted, we also support findings of mutations in the mTOR pathway and receptor tyrosine kinase family genes. MSS CRCs showed higher incidences of mutations in the APC, KRAS and TP53 genes, confirming previous findings. NGS assays may be designed to detect driver mutations for targeted therapeutics and to identify tumors with high mutation loads for potential treatment with immune checkpoint blockade therapies. Further studies may be warranted to elucidate potential targeted therapeutics against mutations in the mTOR pathway and the receptor tyrosine kinase family in MSI-H CRCs as well as the benefit of anti-PD-1 immunotherapy in hypermutated MSS CRCs or other cancers.

Performance characteristics of next-generation sequencing in clinical mutation detection of colorectal cancers.

Activating mutations in downstream genes of the epidermal growth factor receptor (EGFR) pathway may cause anti-EGFR resistance in patients with colorectal cancers. We present performance characteristics of a next-generation sequencing assay designed to detect such mutations. In this retrospective quality assessment study, we analyzed mutation detected in the KRAS, NRAS, BRAF, and PIK3CA genes by a clinically validated next-generation sequencing assay in 310 colorectal cancer specimens. Tumor cellularity and mutant allele frequency were analyzed to identify tumor heterogeneity and mutant allele-specific imbalance. Next-generation sequencing showed precise measurement of mutant allele frequencies and detected 23% of mutations with 2–20% mutant allele frequencies. Of the KRAS mutations detected, 17% were outside of codons 12 and 13. Among PIK3CA mutations, 48% were outside of codons 542, 545, and 1047. The percentage of tumors with predicted resistance to anti-EGFR therapy increased from 40% when testing for only mutations in KRAS exon 2 to 47% when testing for KRAS exons 2–4, 48% when testing for KRAS and NRAS exons 2–4, 58% when including BRAF codon 600 mutations, and 59% when adding PIK3CA exon 20 mutations. Right-sided colorectal cancers carried a higher risk of predicted anti-EGFR resistance. A concomitant KRAS mutation was detected in 51% of PIK3CA, 23% of NRAS, and 33% of kinase-impaired BRAF-mutated tumors. Lower than expected mutant allele frequency indicated tumor heterogeneity, while higher than expected mutant allele frequency indicated mutant allele-specific imbalance. Two paired neuroendocrine carcinomas and adjacent adenomas showed identical KRAS mutations, but only PIK3CA mutations in neuroendocrine carcinomas. Next-generation sequencing is a robust tool for mutation detection in clinical laboratories. It demonstrates high analytic sensitivity and broad reportable range, and it provides simultaneous detection of concomitant mutations and a quantitative measurement of mutant allele frequencies to predict tumor heterogeneity and mutant allele-specific imbalance.

Thirteen X-chromosomal short tandem repeat loci multiplex data from Taiwanese

Study results of variations in the X chromosome are useful tools in researching the genetic diversity of human populations and individual identification. We developed a 13 X chromosomal short tandem repeat (STR) multiplex system (DXS6807, DXS8378, DSX9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7424, DXS101, GATA172D05, HPRTB, DXS8377, DXS7423) amplified in one single polymerase chain reaction. DNA samples of 113 male and 108 female Taiwanese Han subjects were successfully analyzed using this 13 X-STR multiplex system. The distributions of allele frequencies were examined for independence. DXS8377, DXS101, DXS6789, and DXS6809 were found to be the most polymorphic markers in this study. High values of discrimination power and mean exclusion chance without significant evidence of association between these markers were obtained. In conclusion, this 13 X chromosomal STR multiplex system offers considerable forensic efficiency and may be useful in forensic identification casework.

Molecular characterization and PCR diagnosis of Thailand deletion of α‐globin gene cluster

Thailand deletion of α‐Thalassemia (thal) 1 involves the ζ2‐, γζ1‐, α2‐, α1‐, and υ1‐globin genes. In Southeast Asians and Taiwanese, this mutation is the second most common long‐segment deletion of two α‐globin genes, after the Southeast Asian deletion. To define the Thailand deletion breakpoints, we used polymerase chain reaction (PCR) to amplify the normal‐sequence DNA fragments across the breakpoints. The amplified products were sequenced directly or after cloning into pGem®‐3Z or pCR®2.1 vectors. Comparison of the normal and mutant sequences revealed that the 5′ breakpoint lies between nucleotides 1,269 and 1,290 upstream of the initiator codon adenine of the ζ2‐globin gene, and the 3′ breakpoint lies between nucleotides 29,387 and 29,408 downstream of it. A total of 30,677 nucleotides were deleted. Both breakpoints mentioned above lie within the Alu repetitive sequences and an extensive sequence homology is present around the two breakpoints. These findings suggest that homologous recombination is the mechanism by which the deletion occurs. Based on our data, we used three oligonucleotide primers to amplify the regions across the deletion and its corresponding normal sequence. The feasibility of PCR diagnosis was confirmed in 20 carriers with this deletion. Am. J. Hematol. 57:124–130, 1998.