Leukocyte alkaline phosphatase and carcinoembryonic antigen in breast cancer patients: clinical correlation with the markers

Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups

BACKGROUND

Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based on chip or exome genotyping data. Such studies have limitations regarding whole genome-wide association analysis, making it crucial to have genome-to-phenome association information with the largest possible whole genome and matched phenome data to conduct further population-genome studies and develop health care services based on population genomics.

RESULTS

Here, we present 4,157 whole genome sequences (Korea4K) coupled with 107 health check-up parameters as the largest genomic resource of the Korean Genome Project. It encompasses most of the variants with allele frequency >0.001 in Koreans, indicating that it sufficiently covered most of the common and rare genetic variants with commonly measured phenotypes for Koreans. Korea4K provides 45,537,252 variants, and half of them were not present in Korea1K (1,094 samples). We also identified 1,356 new genotype-phenotype associations that were not found by the Korea1K dataset. Phenomics analyses further revealed 24 significant genetic correlations, 14 pleiotropic associations, and 127 causal relationships based on Mendelian randomization among 37 traits. In addition, the Korea4K imputation reference panel, the largest Korean variants reference to date, showed a superior imputation performance to Korea1K across all allele frequency categories.

CONCLUSIONS

Collectively, Korea4K provides not only the largest Korean genome data but also corresponding health check-up parameters and novel genome-phenome associations. The large-scale pathological whole genome-wide omics data will become a powerful set for genome-phenome level association studies to discover causal markers for the prediction and diagnosis of health conditions in future studies.

Leukocyte Alkaline Phosphatase, CA15-3, CA125, and CEA in Cancer Patients

Peripheral blood leukocyte alkaline phosphatase (LAP) scores and CA15-3, CA125, and CEA levels in plasma were measured in 57 patients with metastatic breast, ovarian, and colorectal cancer, respectively, and in 79 patients with the same types of nonmetastatic cancer. The mean LAP scores of the metastatic cancer patients (261, 272 and 275 for breast, ovary and colon, respectively) were significantly higher than those of the nonmetastatic cancer group (70, 68 and 57, respectively). There was no overlap between the 95% confidence intervals of the two groups (i.e., metastatic versus nonmetastatic), and no patient known to be metastatic had a LAP score within the normal range. The mean levels of other markers in the metastatic patients (CA15-3, 63.4 μ/ml; CA125, 104.8 μ/ml; and CEA, 51.8 ng/ml for metastatic breast, ovarian, and colon cancer, respectively) were also higher than in the nonmetastatic patients (CA15-3, 24 μ/ml; CA125, 25.3 μ/ml; and CEA, 5.8 ng/ml for nonmetastatic breast, ovarian, and colon cancer, respectively). However, the 95% confidence intervals of the nonmetastatic and the metastatic patients overlapped so that there were false-negatives and/or false-positives when the other markers were used. We therefore conclude that the addition of the LAP score to conventional cancer markers could be helpful for the diagnosis of recurrence and follow-up of cancer patients and suggest that our results be confirmed by further studies on a larger series of patients.

Leukocyte Alkaline Phosphatase and Carcinoembryonic Antigen in Metastatic Colorectal Cancer Patients

Peripheral blood leukocyte alkaline phosphatase scores and plasma carcinoembryonic antigen levels in 26 patients with metastatic colorectal cancer were compared to those in 30 healthy controls. Patients had metastases to the liver and abdomen. The mean leukocyte alkaline phosphatase score in the metastatic colorectal cancer patients was significantly higher than in the control group (246 ± 65 vs, 52 ± 26, p < 0.001); and the mean carcinoembryonic antigen level in the patients was also significantly higher than in the controls (110 ± 100 vs, 4.9 ± 3 ng/ml, p < 0.001). One hundred percent of the metastatic cancer patients had elevated LAP scores and 73% of these patients had elevated CEA levels. There was a difference between the mean CEA levels in the patients with liver metastases and those with abdominal metastases (162 ± 135 vs, 39 ± 53 ng/ml, p < 0.04). The results suggest that although both markers are elevated in metastatic colorectal cancer, the LAP score seems to be more useful in detecting metastatic disease, since we found 11 % false negatives with the CEA level and 0 % false negatives with the LAP score.

Leukocyte alkaline phosphatase score in patients with cerebrovascular disease and in patients with primary and metastatic brain tumors

Leukocyte alkaline phosphatase (LAP) activity in peripheral blood was determined in 54 patients with cerebrovascular disease (CVD), 11 patients with primary brain tumor, and 23 patients with metastatic brain tumor. The LAP score of the primary brain tumor patients (155 +/- 40) was significantly higher (P less than 0.03) than the LAP score for cerebrovascular disease patients (96 +/- 87). The LAP score levels of the metastatic brain tumor patients (251 +/- 55) was significantly higher as compared with both the cerebrovascular disease (P less than 0.001) and primary brain tumor groups (P less than 0.001). The LAP score could serve as an additional, although non-specific, marker to assist in the differentiation between cerebrovascular disease and brain tumors.