
Genome-wide association studies: inherent limitations and future challenges
Yan Du, Jiaxin Xie, Wenjun Chang, Yifang Han, Guangwen Cao
Front. Med. ›› 2012, Vol. 6 ›› Issue (4) : 444-450.
Genome-wide association studies: inherent limitations and future challenges
Genome-wide association studies (GWAS) have achieved great success in identifying genetic variants related to complex human diseases such as cancer and have provided valuable insights into their genetic architecture. Recently, GWAS is quite the fashion in China. However, there are issues related to its nature. Enormous work needs to be done in the post-GWAS era. Deep sequencing followed by functional studies will be needed to elucidate the underpinning biological mechanisms and further translate GWAS findings into medical practice. Along with pharmacogenomics, the success of GWAS in identifying genetic risk factors and genetic differences in drug response has been gradually enabling personalized medicine. In this article, we used hepatocellular carcinoma (HCC) as an example to demonstrate some of the inherent limitations and summarized future challenges of GWAS.
genome-wide association studies (GWAS) / genetic variant / cancer / limitation / challenge
Tab.1 Full inclusion and exclusion criteria |
Inclusion criteria | Exclusion criteria | |
---|---|---|
Population | Studies will be included if they are: ● Human studies without any limitation on age, geography, gender, and type of disease | Focus exclusively on: ● Non-human studies |
Concept | Studies will be included if they are: ● RCTs of any one of four NPTCM (e.g., acupuncture, moxibustion, cupping, or Tuina/massage) | Focus exclusively on: ● Study interventions other than the four NPTCM (e.g., acupuncture, moxibustion, cupping, or Tuina/massage). OR ● Combined more than two studied interventions, or combined any other types of NPTCM interventions. OR ● Non-randomized or quasi-randomized controlled trials. OR ● Non-controlled trials. OR ● Observational studies. OR ● Case reports. OR ● Study protocols. OR ● Reviews |
Context | Studies were included if they are: ● Published in English or Chinese. AND ● Published from 01/01/2022 to 31/12/2022 | Focus exclusively on: ● Studies without abstracts or full text are not available. OR ● Repeat publications |
Tab.2 Geographical distribution of the included studies (n = 387) |
Geographical distribution | n (%) |
---|---|
China | 368 (95.1) |
South Korea | 4 (1.0) |
USA | 3 (0.8) |
Iran | 2 (0.5) |
Spain | 2 (0.5) |
Austria | 1 (0.3) |
Egypt | 1 (0.3) |
Germany | 1 (0.3) |
Indonesia | 1 (0.3) |
Lebanon | 1 (0.3) |
Malaysia | 1 (0.3) |
Pakistan | 1 (0.3) |
Poland | 1 (0.3) |
Turkey | 1 (0.3) |
Tab.3 Information of the included studies (n = 387) |
Information | Acupuncture n (%) | Moxibustionn (%) | Tuina/massagen (%) | Cuppingn (%) | Totaln (%) |
---|---|---|---|---|---|
Part 1 Information of included articles and journals | |||||
Language of publications | |||||
English | 22 (5.7) | 2 (0.5) | 8 (2.1) | 0 | 32 (8.3) |
Chinese | 191 (49.4) | 71 (18.3) | 77 (19.9) | 16 (4.1) | 355 (91.7) |
Type of journalsa | |||||
English journal (SCIE), with impact factor > 3 | 8 (2.1) | 0 | 3 (0.8) | 0 | 11 (2.8) |
Chinese core journal | 25 (6.5) | 3 (0.8) | 1 (0.3) | 1 (0.3) | 30 (7.8) |
Part 2 Participants | |||||
Type of disease/pattern(s) (top 3)b | |||||
Diseases of the musculoskeletal system or connective tissue | 51 (13.2) | 14 (3.6) | 18 (4.7) | 4 (1.0) | 87 (22.5) |
Diseases of the nervous system | 59 (15.2) | 7 (1.8) | 6 (1.6) | 3 (0.8) | 75 (19.4) |
Symptoms, signs or clinical findings, not elsewhere classified | 35 (9) | 7 (1.8) | 17 (4.4) | 2 (0.5) | 61 (15.8) |
Including CM pattern(s) | 34 (8.8) | 25 (6.5) | 9 (2.3) | 6 (1.6) | 74 (19.1) |
Type of CM pattern(s) (top 3)c | |||||
Pattern(s) of qi stagnation and blood stasis | 6 (1.6) | 1 (0.3) | 2 (0.5) | 2 (0.5) | 11 (2.8) |
Pattern(s) of liver and kidney depletion | 4 (1.0) | 0 | 1 (0.3) | 0 | 5 (1.3) |
Pattern(s) of qi deficiency with blood stasis | 3 (0.8) | 0 | 1 (0.3) | 0 | 4 (1.0) |
Age design of participants | |||||
< 18 years old | 4 (1.0) | 6 (1.6) | 18 (4.7) | 3 (0.8) | 31 (8.0) |
≥ 18 years old | 209 (54.0) | 67 (17.3) | 66 (17.1) | 12 (3.1) | 354 (91.5) |
Any age | 0 | 0 | 1 (0.3) | 1 (0.3) | 2 (0.5) |
Total sample size | |||||
≤ 50 | 19 (4.9) | 9 (2.3) | 9 (2.3) | 1 (0.3) | 38 (9.8) |
51–100 | 147 (38) | 53 (13.7) | 52 (13.4) | 12 (3.1) | 264 (68.2) |
101–200 | 38 (9.8) | 10 (2.6) | 19 (4.9) | 3 (0.8) | 70 (18.1) |
> 200 | 9 (2.3) | 1 (0.3) | 5 (1.3) | 0 | 15 (3.9) |
Part 3 Study design | |||||
Study purpose | |||||
Efficacy | 147 (38.0) | 55 (14.2) | 71 (18.3) | 14 (3.6) | 287 (74.2) |
Both (efficacy and safety) | 66 (17.1) | 18 (4.7) | 14 (3.6) | 2 (0.5) | 100 (25.9) |
Number of assigned groups | |||||
2 | 193 (49.9) | 70 (18.1) | 78 (20.2) | 15 (3.9) | 356 (92.0) |
3 | 18 (4.7) | 3 (0.8) | 5 (1.3) | 1 (0.3) | 27 (7.0) |
4 | 2 (0.5) | 0 | 2 (0.5) | 0 | 4 (1.0) |
Trial participating center | |||||
Single center | 198 (51.2) | 68 (17.6) | 82 (21.2) | 14 (3.6) | 362 (93.5) |
Multicenter | 15 (3.9) | 5 (1.3) | 3 (0.8) | 2 (0.5) | 25 (6.5) |
Type of randomizationd | |||||
Simple randomization | 201 (51.9) | 72 (18.6) | 79 (20.4) | 16 (4.1) | 368 (95.1) |
Others | 12 (3.1) | 1 (0.3) | 6 (1.6) | 0 | 19 (5.0) |
Type of blinding | |||||
Open label | 3 (0.8) | 0 | 0 | 0 | 3 (0.8) |
Blinding | 38 (9.8) | 7 (1.8) | 4 (1.0) | 1 (0.3) | 50 (12.9) |
Not reported | 172 (44.4) | 66 (17.1) | 81 (20.9) | 15 (3.9) | 334 (86.3) |
Part 4 Interventions | |||||
Types and duration | |||||
Single intervention | 120 (31) | 34 (8.8) | 32 (8.3) | 7 (1.8) | 193 (49.9) |
Complex interventions | 93 (24) | 39 (10.1) | 53 (13.7) | 9 (2.3) | 194 (50.1) |
Treatment duration (week, mean) | 4.9 | 4.1 | 5.2 | 3.1 | 4.8 |
Part 5 Comparisons | |||||
Type of controlse | |||||
Including placebo control | 20 (5.2) | 1 (0.3) | 2 (0.5) | 0 | 23 (5.9) |
Part 6 Outcomes | |||||
Including CM pattern-related outcome(s) | 16 (4.1) | 6 (1.6) | 6 (1.6) | 4 (1.0) | 32 (8.3) |
Part 7 Funding, registration, and protocol | |||||
Including funding supports | 147 (38.0) | 42 (10.9) | 40 (10.3) | 8 (2.1) | 237 (61.2) |
Including registration | 22 (5.7) | 5 (1.3) | 8 (2.1) | 1 (0.3) | 36 (9.3) |
Including protocol | 17 (4.4) | 2 (0.5) | 6 (1.6) | 0 | 25 (6.5) |
aThe journal types and impact factors of English journals were based on the latest data on the official website of Journal Citation Reports. Chinese core journals were according to the latest data of CNKI official website. Detailed rules are presented in supplementary file 6.1. bAccording to the International Classification of Diseases 11th Revision (ICD-11) in 2023. More details are presented in the supplementary file 6.3. cThis item is based on the 74 studies which reported type of CM pattern(s). The total number of patterns 94 exceeded 74 because more than one type of pattern was reported in several studies. The percentage was based on the number of included studies 387. More details are presented in the supplementary file 6.4. dOther types of randomization included stratified randomization, central randomization, and minimization randomization. eThe total number of control types 394 exceeded the number of included studies 387 because several studies have more than two control groups. The percentage was based on the number of included studies 387. More details are presented in the supplementary file 6.5. |
Tab.4 Adverse events identified in the included studies (n = 387) |
Classification | Acupuncture n (%) | Moxibustionn (%) | Tuina/massagen (%) | Cuppingn (%) | Totaln (%) |
---|---|---|---|---|---|
Including adverse events (AEs) assessment in the studya | 42 (11.1) | 6 (1.6) | 7 (1.9) | 1 (0.3) | 56 (14.8) |
Including AEs reports in the experimental groupb | 39 (70.0) | 6 (10.7) | 5 (8.9) | 1 (1.8) | 51 (91.2) |
AEs related to the interventionc | 19 (37.3) | 0 | 0 | 0 | 19 (37.3) |
Specific syndromesd | |||||
Skin damage (e.g., rash, itching, etc.) | 26 (17.2) | 2 (1.3) | 1 (0.7) | 1 (0.7) | 30 (19.9) |
Digestive system damage (e.g., nausea, vomiting, diarrhea, constipation, abnormal liver function, etc.) | 7 (4.6) | 5 (3.3) | 2 (1.3) | 0 | 14 (9.3) |
Urinary system damage (e.g., hematuria, renal dysfunction, etc.) | 0 | 1 (0.7) | 0 | 0 | 1 (0.7) |
Systemic damage (e.g., anaphylactic shock, fever, etc.) | 15 (9.9) | 3 (19.9) | 3 (2.0) | 0 | 21 (13.9) |
No AE was identified in the experimental group | 3 (2.0) | 0 | 2 (1.3) | 0 | 5 (3.3) |
aThe percentage was based on the number (387) of included studies. bThe percentage was based on the number (56) of studies including AEs reports in the experimental and control groups. cThe percentage was based on the number (51) of studies including AEs reports in the experimental group. dThe number of AEs in the experimental and control groups was 151 from the 56 studies that reported the AEs. It exceeded 56 because more than one type of AE was reported in several studies. The percentage was based on the number (151) of AEs in the experimental group. More details of AEs in the control group are presented in the supplementary file 6.6. |
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