diff --git a/R/genotype_io.R b/R/genotype_io.R
index 8774385d..8fecfdc6 100644
--- a/R/genotype_io.R
+++ b/R/genotype_io.R
@@ -460,7 +460,7 @@ computeBlockLdCor <- function(handle, snp_idx, backend = "internal",
 
   ext <- tolower(file_ext(path))
   if (nzchar(ext)) {
-    return(switch(ext,
+    detected <- switch(ext,
       "vcf" = "vcf",
       "bcf" = "vcf",
       "bed" = "plink1",
@@ -475,16 +475,19 @@ computeBlockLdCor <- function(handle, snp_idx, backend = "internal",
       "annot" = "ldsc_annot",
       "bw" = "bigwig",
       "bigwig" = "bigwig",
-      stop("Cannot detect format from extension: ", ext)
-    ))
+      NULL
+    )
+    if (!is.null(detected)) return(detected)
   }
-  # No extension — check for plink stem files
+  # Check for file stems, including dotted prefixes such as sample.EUR.chr21.
   if (file.exists(paste0(path, ".pgen")) || file.exists(paste0(path, ".pvar")))
     return("plink2")
   if (file.exists(paste0(path, ".bed")) || file.exists(paste0(path, ".bim")))
     return("plink1")
   if (file.exists(paste0(path, ".gds")))
     return("gds")
+  if (nzchar(ext))
+    stop("Cannot detect format from extension: ", ext)
   stop("Cannot detect genotype format for path: ", path)
 }
 
diff --git a/tests/testthat/test_load_genotype.R b/tests/testthat/test_load_genotype.R
index 8ca761d7..60854574 100644
--- a/tests/testthat/test_load_genotype.R
+++ b/tests/testthat/test_load_genotype.R
@@ -13,6 +13,15 @@ region_sub <- "chr21:17513228-17550000"
 n_samples <- 100L
 n_variants <- 349L
 
+test_that("format detection supports dotted PLINK2 prefixes", {
+  tmp <- tempfile("plink2_dotted_prefix_")
+  prefix <- file.path(dirname(tmp), "ADSP.R4.EUR.chr21")
+  file.create(paste0(prefix, ".pgen"), paste0(prefix, ".pvar"), paste0(prefix, ".psam"))
+  on.exit(unlink(paste0(prefix, c(".pgen", ".pvar", ".psam"))), add = TRUE)
+
+  expect_equal(pecotmr:::.h2_detect_format(prefix), "plink2")
+})
+
 # Shared helper: validate the output structure from load_genotype_region
 # (with return_variant_info=TRUE)
 check_genotype_result <- function(result, expected_nrow = n_samples, expected_ncol = n_variants,